Winger Anthony D'Souza (39th minute) put Pune FC ahead in the first half before strikes from striker Chidi Edeh (72nd) and substitute Seimilen Doungel (75th) handed East Bengal all three points.
Pune FC's third consecutive loss means they stay in the seventh place with 31 points.
Coach Mike Snoei made five changes to the line-up handing starts to Anas Edathodika, Zohmingliana Ralte, Mumtaz Akhtar, Anthony D'Souza and Thongkhosiem Haokip.
Twenty-two minutes in, East Bengal created the first close chance of the match. With playmaker Sueoka getting into the clear on the left inside the box miscommunication in the defense, his shot from point-blank range was saved by 'keeper Amrinder Singh.
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Ten minutes later, medio Subodh Kumar's 30-yard effort cames of the woodwork as East Bengal started to push.
At the other end, after several half chances, Pune FC finally took the lead in the 39th minute. Attacker Riga Mustapha found Haokip on the edge of the box down the center. The young striker sent a cheeky through ball to Anthony inside the box who calmly slotted home from close range
The hosts came out all guns blazing in the second half creating chance after chance. However, some stubborn goalkeeping by East Bengal custodian Gurpreet Singh kept the visitors in the game.
Minutes after the hour mark, the tall keeper saved defender Calum Angus' powerful freekick but the rebound fell back for the Englishman whose volley flew over.