Both teams had their chances in the game but it was left to Marcelinho to give the hosts the lead in the 74th minute with a long-range effort.
And it was left to substitute Marko Stankovic to seal the three points in injury time from the spot after he himself had been brought down by FC Goa defender Mohamed Ali.
FC Goa drop behind in the ISL playoff race, while FC Pune City move closer to the top teams.
FC Goa next host NorthEast United FC at home on December 14, while FC Pune City will play their next match in 2019.
MATCH AWARDS
Club Award – FC Pune City
Swift Limitless Player of the Match – Ahmed Jahouh (FC Goa)
DHL Winning Pass of the Match – Sarthak Golui (FC Pune City)
ISL Emerging Player of the Match – Kamaljit Singh (FC Pune City)
Hero of the Match – Marcelo Pereira (FC Pune City)