After missing Schalke’s previous two games, the former Tottenham Hotspur midfielder returned to Domenico Tedesco’s squad and made an impact after his introduction in the second period.
Guido Burgstaller put the visitors ahead at the BayArena with a brilliant finish in the 11th minute.
With just few minutes remaining in the encounter, Bentaleb, a 66th-minute substitute, sent goalkeeper Bernd Leno the wrong way from the penalty spot in the 85th minute after Breel Embolo was upeneded in the penaty area.
The 23-year-old has now scored four goals in eight appearances in the German top-flight this season.
The win moved Schalke 04 to the third spot in the German top-flight table with 50 points from 24 games and they host Hertha Berlin for their next outing on March 3.