A 20-yard strike from Marcelinho in the 74th minute and an injury-time penalty by Marko Stankovic were enough to see off the Gaurs.
FC Pune City interim coach Pradhyum Reddy replaced the suspended Sahil Panwar with Martin Diaz to form a three-man defence.
On the other side, Sergio Lobera brought back skipper Mandar Rao Dessai in place of Carlos Pena. Mohamed Ali stepped in place of Chinglensana Singh and Hugo Boumous returned from suspension to replace Jackichand Singh.
Brandon Fernandes forced Kamaljit Singh into making his first save in the 22nd minute as Goa tried to convert their dominance to goals.
It didn't take long for Edu Bedia to get into the thick of the action but the closest he could get to scoring was when he hit the crossbar and the first-half ended goallessly.
Coro was kept silent throughout the match but he did manage to dance his way into the Pune box in the 54th minute, but his shot was blocked by Adil Khan.
Nim Dorjee Tamang headed Kuruniyan's teasing cross from the left straight towards Nawaz in Pune's first attempt at goal in the second half.
Both goalkeepers were at their best on the evening as Kamaljit kept out a powerful shot by Jahouh from outside the box before Nawaz dived to his right to deflect wide Marcelinho's shot on target in the 71st minute.
However, there was no stopping Marcelinho's rasping shot from about 20 yards out in the 74th minute. Sarthak Golui found the striker in space outside the box and the Brazilian unleashed a beautiful, swerving shot into the net.
In the very next minute, Goa rattled the woodwork for the second time after Jahouh tried to curl the ball into the net but the league's top goalscorers failed to find a way back into the net.
Mohammad Ali grabbed hold of Marko Stankovic inside the box and the foul was punished with a penalty. The midfielder scored to seal three points for his side.