The Royal Blues had a first half lead but succumbed to Pep Guardiola's men who ended the encounter at the Veltins-Arena with 10 men.
Aguero opened the scoring in the 18th courtesy of David Silva's assist but Bentaleb inspired the hosts' fight-back with two goals from the spot before the interval.
After the Video Assistant Referee adjudged Nicolas Otamendi to have touched a goal-bound shot with his hand, the 24-year-old stepped forward and converted his effort to draw both sides levelled in the 38th minute.
Seven minutes later, the midfielder converted from the spot again after Fernandinho tripped Senegalese defender Salif Sane in the penalty area to put Domenico Tedesco's side ahead.
The two goals took Bentaleb's tally to three goals, including his goal from the penalty spot against Schalke 04, in five Uefa Champions League outings this season.
Despite Otamendi's expulsion in the 68th minute, goals from Leroy Sane and Raheem Sterling in the last five minutes of the encounter handed the Premier League champions a first leg advantage over their Bundesliga opponent.