The Algeria international made an instant impact two minutes after replacing Suat Serdar at the Volkswagen Arena.
Bentaleb's effort from the penalty spot in the 85th minute cancelled out John Brooks' opener in the 33rd minute.
The encounter was heading for a stalemate until Daniel Ginczek's 94th-minute effort dented Schalke's hopes of grabbing a point.
Bentaleb has now scored two goals in two games this season - including his effort in the German Cup win over Schweinfurt last Saturday.
Ghana's Abdulrahman Baba played for 90 minutes for the first time since the 2016-17 season while Senegal's Salif Sane made his league bow for Schalke after moving from Hannover 96 at the end of last campaign.