Kevin-Prince Boateng enjoyed game time for Schalke as they lost 3-0 against Dortmund in the Revierderby on Saturday.
The Ghanaian international was replaced after 64 minutes by Barnetta as they suffered the setback at the Signal-Iduna-Park.
The Royal Blues had looked impressive of late too, with just one defeat in their last six Bundesliga games helping Roberto Di Matteo's side march to fourth place in the German top division.
But goals from Aubameyang, Mkhitaryan and Reus left them gasping for breath.
But sides have struggled in the Champions League over the past couple of weeks, with Schalke losing to Real Madrid and Dortmund to Juventus.
Dortmund are up and running after a difficult start to the season and lie 9th on the league table.