Darko Nikac, Luciano Sobrosa and Thongkhosiem Haokip were on the scoresheet for the visitors before Eugeneson Lyngdoh pulled one back for the home side.
Nine minutes into the game, it was Pune FC who took the lead as Montenegrin striker Darko Nikac slotted the ball past rival goalkeeper Lalthuammawia Ralte with a brilliant effort.
Before the home side could make any inroads Pune FC doubled their lead as Brazilian Luciano Sobrosa found the top corner from a Marcelino's delivery in the 25 minutes into the game.
In the second half, Bengaluru tried to comeback by bringing in the experienced Sunil Chettri on the field but lack of constructive play near the box, resulted in creation of very few chances.
Pune's third goal came through Thongkhosiem Haokip's whose shot hit the top of the cross bar and crossed the goal line.
The Bengaluru side was only able to pull back a consolation goal through Eugeneson Lyngdoh
The win took Pune FC's tally to four points from matches while Bengaluru FC have a point to show from as many matches.
In another encounter, Kalyani Bharat FC played out a goal-less against Dempo Sports Club.