Winger Gilbert Oliveira (38th minute) gave Salgaocar FC the lead before Riga Mustapha (56th) equalised from the penalty spot for Pune FC early on in the second half.
Striker Daryll Duffy (84th) then scored in the final ten minutes to hand Salgaocar a win.
Pune FC played majority of the second half with ten men after medio Dhanpal Ganesh was shown a straight red card in the 54th minute.
With this loss Pune FC stay in sixth place with 31 points from 21 games.
Pune FC began the better of the two sides with winger Anthony D'Souza and attacker Riga forcing Salgaocar custodian Karanjit Singh into early saves.
At the other end, striker Dudu Omagbemi's header from close range went over after the Nigerian did well to connect Freiman Peixoto.
Five minutes past the half hour mark, Anthony did well to beat his marker on the edge of the box and chipped in a cross for Riga whose attempt was saved by the keeper.
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