Kane's penalty was his seventh goal in qualifying
England must wait to confirm their place in Euro 2020 after the Czech Republic deservedly ended their 43-game unbeaten run in qualifiers stretching back 10 years.
Gareth Southgate's side would have secured their place in next summer's tournament with victory in Prague but they can have no complaints after a wretched display against a Czech side who were a different proposition from that swept aside 5-0 at Wembley in March.
England can still qualify on Monday if they beat Bulgaria and Kosovo do not beat Montenegro.
England were handed the perfect start when captain Harry Kane put them ahead from the penalty spot in the fifth minute after Lukas Masopust fouled Raheem Sterling but they were well below their best and slumped to a bitterly disappointing defeat.
The Czechs were swiftly level when Jakub Brabec scored following a corner. England could not muster further inspiration and substitute Zdenek Ondrasek pounced to score the winner with four minutes left.
England were desperately poor throughout and were grateful to goalkeeper Jordan Pickford, who produced fine saves from Vladimir Coufal, Masopust and Alex Kral, while Czech counterpart Tomas Vaclik did well to deny Sterling and Kane.
They can put things right against Bulgaria in Sofia on Monday but this was a serious reality check for a side hoping to do great things next summer, losing a qualifier for the first time since they went down 1-0 to Ukraine on 10 October 2009.
- Relive England's defeat in the Czech Republic
England deserve no better
This must rank as one of the worst performances of Southgate's reign and the manager himself has to take his own share of the responsibility.
No-one can complain about his decision to give Chelsea's in-form Mason Mount his debut ahead of team-mate Ross Barkley but the youngster never flourished in an advanced midfield position in the first half.
Quality sides will relish facing this England defence and Southgate is running out of time to apply the fix
Mount was barely able to influence the game and with Jordan Henderson and Declan Rice exposed and pedestrian, England found themselves often overrun by the sprightly Czechs.
England's potent attacking trio of Kane, Sterling and Jadon Sancho were starved of service, leaving them under-performing in every area of the pitch.
The Czech Republic, backed by a noisy crowd in Prague, gathered momentum and confidence and it was no surprise when Ondrasek finally broke Pickford's resistance late on.
This was simply not good enough from England and the concerns that surfaced about their true quality when they won 5-3 in chaotic style against Kosovo in Southampton will only increase after this.
Defensive woes continue
Any hope the defensive uncertainty that characterised England's victory against Kosovo had been successfully addressed was banished inside the first 10 minutes in Prague.
Pickford saved brilliantly from Coufal as the Czech Republic responded to England's early salvo but there was the trademark confusion at the resulting corner which ended with Brabec stabbing home from close range.
England lived dangerously throughout and it was not a shock when they finally conceded late on.
Everton's Michael Keane struggles desperately at this level while full-backs Danny Rose and Kieran Trippier hardly covered themselves in glory either.
Harry Maguire looks the one staple in defence but he does not exude confidence either.
In other words, quality sides will relish facing this England defence and Southgate is running out of time to apply the fix.
More to follow.
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Line-ups
Match Stats
Live Text
Line-ups
Czech Rep
1Vaclik
5Coufal
3Celustka
4Brabec
18Boril
15Soucek
21Kral
20MasopustSubstituted forZmrhalat 90'minutes
8Darida
14JanktoBooked at 8minsSubstituted forKopicat 83'minutes
19SchickSubstituted forOndrasekat 65'minutes
Substitutes
2Reznik
6Kudela
7Krejci
9Ondrasek
10Husbauer
11Krmencik
12Kalvach
13Kopic
16Kolar
17Zmrhal
22Simic
23Pavlenka
England
1Pickford
2Trippier
5Keane
6Maguire
3RoseBooked at 10mins
8HendersonBooked at 90mins
4RiceSubstituted forAbrahamat 88'minutes
10SanchoSubstituted forRashfordat 73'minutes
11MountSubstituted forBarkleyat 72'minutes
7SterlingBooked at 68mins
9Kane
Substitutes
12Alexander-Arnold
13Pope
14Chilwell
15Gomez
16Mings
17Tomori
18Winks
19Barkley
20Rashford
22Henderson
23Abraham
Referee:
Damir Skomina
Match Stats
Home TeamCzech RepAway TeamEngland
Possession
Home44%
Away56%
Shots
Home17
Away7
Shots on Target
Home8
Away4
Corners
Home6
Away2
Fouls
Home15
Away10
Live Text
Posted at
Match ends, Czech Republic 2, England 1.
Full TimePosted at 90'+5'
Second Half ends, Czech Republic 2, England 1.
Posted at 90'+5'
Attempt saved. Jan Kopic (Czech Republic) left footed shot from the centre of the box is saved in the top left corner. Assisted by Jaromir Zmrhal.
BookingPosted at 90'+2'
Jordan Henderson (England) is shown the yellow card for a bad foul.
Posted at 90'+2'
Ross Barkley (England) wins a free kick in the defensive half.
Posted at 90'+2'
Foul by Vladimír Darida (Czech Republic).
Posted at 90'
Harry Maguire (England) wins a free kick in the defensive half.
Posted at 90'
Foul by Zdenek Ondrasek (Czech Republic).
SubstitutionPosted at 90'
Substitution, Czech Republic. Jaromir Zmrhal replaces Lukas Masopust.
SubstitutionPosted at 88'
Substitution, England. Tammy Abraham replaces Declan Rice.
Goal!Posted at 85'
Goal! Czech Republic 2, England 1. Zdenek Ondrasek (Czech Republic) right footed shot from the centre of the box to the bottom right corner. Assisted by Lukas Masopust.
Posted at 83'
Danny Rose (England) wins a free kick on the left wing.
Posted at 83'
Foul by Alex Kral (Czech Republic).
SubstitutionPosted at 83'
Substitution, Czech Republic. Jan Kopic replaces Jakub Jankto.
Posted at 81'
Corner, England. Conceded by Jan Boril.
Posted at 81'
Attempt saved. Harry Kane (England) right footed shot from a difficult angle on the right is saved in the centre of the goal. Assisted by Ross Barkley with a through ball.
Posted at 79'
Raheem Sterling (England) wins a free kick on the right wing.
Posted at 79'
Foul by Jan Boril (Czech Republic).
Posted at 78'
Corner, Czech Republic. Conceded by Jordan Pickford.
Posted at 78'
Attempt saved. Alex Kral (Czech Republic) right footed shot from the right side of the box is saved in the top right corner. Assisted by Vladimír Darida.
Posted at 75'
Foul by Kieran Trippier (England).
Posted at 75'
Jakub Jankto (Czech Republic) wins a free kick on the left wing.
Posted at 74'
Attempt missed. Vladimír Darida (Czech Republic) left footed shot from outside the box misses to the right.
SubstitutionPosted at 73'
Substitution, England. Marcus Rashford replaces Jadon Sancho.
SubstitutionPosted at 72'
Substitution, England. Ross Barkley replaces Mason Mount.
BookingPosted at 68'
Raheem Sterling (England) is shown the yellow card.
Posted at 68'
Foul by Raheem Sterling (England).
Posted at 68'
Jakub Brabec (Czech Republic) wins a free kick in the defensive half.
Posted at 66'
Corner, Czech Republic. Conceded by Declan Rice.
Posted at 65'
Attempt saved. Jordan Henderson (England) right footed shot from outside the box is saved in the bottom right corner. Assisted by Mason Mount.
SubstitutionPosted at 65'
Substitution, Czech Republic. Zdenek Ondrasek replaces Patrik Schick.
Posted at 64'
Attempt saved. Harry Kane (England) right footed shot from the centre of the box is saved in the centre of the goal. Assisted by Raheem Sterling.
Posted at 60'
Corner, Czech Republic. Conceded by Jordan Pickford.
Posted at 59'
Attempt saved. Lukas Masopust (Czech Republic) left footed shot from outside the box is saved in the top centre of the goal. Assisted by Vladimir Coufal.
Posted at 59'
Foul by Harry Maguire (England).
Posted at 59'
Vladimir Coufal (Czech Republic) wins a free kick in the defensive half.
Posted at 58'
Jordan Henderson (England) wins a free kick in the attacking half.
Posted at 58'
Foul by Vladimír Darida (Czech Republic).
Posted at 56'
Foul by Mason Mount (England).
Posted at 56'
Vladimir Coufal (Czech Republic) wins a free kick in the defensive half.
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goal
Source: bbc.com