Adil Khan gave Pune the lead in the 35th minute before Venezuelan forward Miku (64th, 78th) struck twice in the second half to hand the advantage to Bengaluru.
Bengaluru captain Sunil Chhetri hammered the final nail in Pune's coffin in the final minute.
The result sees Bengaluru take the sole lead with 12 points from five matches.
Pune, meanwhile, are at the fourth position with nine points. Second placed FC Goa and third placed Chennaiyin FC also have a similar points tally, but have better goal differences than Pune.
Pune looked like the better side in the first 45 minutes with Khan giving then the lead shortly before half-time.
The match, however, turned on its head in the second session after Pune defender Baljit Singh was sent off for a second yellow card in the 56th minute.
ISL debutants Bengaluru did not look entirely convincing in the first session as they gave away the ball cheaply and looked fragile at the back. Their defensive line also made uncharacteristic mistakes, giving Pune a clear look at the goal.
Bengaluru had just one shot on goal in the first session. Chhetri did manage to fing the back of the net, but his attempt was ruled out due to handball.
Pune, who had top scorer Marcelinho on the bench, surged ahead thanks to some brilliant work from Isaac Vanmalsawma. Midfielder Marcos Tebar kick-started the attack and found Vanmalsawma on the left. Vanmalsawma crossed the ball into the heart of the Bengaluru defence where nobody saw Khan burst from nowhere and finish with a superb diving effort.
Bengaluru have scored seven of their 10 goals in the second session. Understandably they attacked with vigour in the second half and were helped by the sending off of Baljit, the second time in as many matches that Pune had a player red-carded.
Bengaluru's equaliser came through Miku, their highest scorer. Chhetri moved in from the left and saw Edu Garcia overlapping. He rolled the ball swiftly and the Spaniard simply pulled it back for Miku to finish from close range.
Miku scored his, and the team's, second goal with another exquisite finish after Garcia's attempt was blocked by a rival defender.
Chhetri then made the best use of Pune's tired legs as he ran to meet a through-ball from Toni Dovale and calmly lifted it over the on-rushing goalkeeper, deep into added time.
(This story has not been edited by Social News XYZ staff and is auto-generated from a syndicated feed.)
About VDC
Doraiah Chowdary Vundavally is a Software engineer at VTech . He is the news editor of SocialNews.XYZ and Freelance writer-contributes Telugu and English Columns on Films, Politics, and Gossips. He is the primary contributor for South Cinema Section of SocialNews.XYZ. His mission is to help to develop SocialNews.XYZ into a News website that has no bias or judgement towards any.