With the Mohun Bagan defence caught napping, Milan Singh Ongnam put the Pune outfit ahead in the 33rd minute but the Mariners nosed ahead with Balwant's double strikes (42nd and 44th) from Pritam Kotal assists at the Rabindra Sarovar Stadium.
Mohun Bagan earned a penalty in the 87th minute after Gourmangi Singh brought down substitute Jeje Lalpekhlua and captain Katsumi Yusa (89th) minute sealed the issue with Shivajians veteran goalkeeper Subrata Paul diving the other way.
Both the Kolkata heavyweights now occupy the top two places with an identical six wins and three draws and they remained unbeaten after nine matches.
There were some early pressure from Mohun Bagan but it was the Pune outfit that drew the first blood after its Spanish midfielder Juan Quero, from the left wing, beat Eduardo Ferreira and set up Milan with a low cross.
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The Manipuri also showed a fine presence of mind by not falling into the offside trap as he surged forward before striking with a first-touch goal to put Mohun Bagan under pressure.
Kotal produced two measured passes from the right wing and Hero of the Match Balwant seized the opportunities on both occasions for his double.
Kotal's cross from a Sony Norde back pass was parried off wrongly into open space by the Pune goalkeeper Paul and Balwant easily headed it into the open net.
In an action replay, Kotal once again set it up and this time Balwant was on the floor and blasted the ball into the top of the right corner with a powerful low volley.
In a 56th minute move, Balwant was set up by Yusa Katsumi from the left but the star of the match was late in his shot.
Kotal once again fed Balwant in the 59th minute from the right but his shot again ballooned over.
Applying pressure in the second half, Norde cut back from left to set up Balwant for a hattrick in front of the goal mouth, but he missed his chance.
Shivajians earned a freekick as they nearly equalised in the 82nd minute but their Irish recruit Shane McFaul's flick went wide.