With this win, Pune kept their hopes alive of reaching the knockout stage as they are firmly placed at the third spot with 19 points, one behind second-placed Chennaiyin FC and two adrift of Bengaluru FC.
Sunil Chhetri scored in the 43rd and 52nd minute to help his team beat Mumbai City FC 3-1.
Bengaluru FC suffered their fourth defeat of the Indian Super League season.
Chennaiyin FC rode on Gregory Nelson's 83rd minute strike to post a 1-0 win over FC Pune City in an Indian Super League (ISL) match at the Jawaharlal Nehru Stadium.
Zequinha was the star of the show, striking in the 73rd minute to give his side the lead and the winner.
After this win, FC Goa have collected 16 points from nine matches, the same as Pune City but are placed behind them in fourth place. While Jamshedpur FC remained on 10 points from nine matches and are placed seventh.
Hume scored in the 12th, 78th and 83rd minute respectively as Kerala elevated themselves to the sixth position.
Resilient Delhi Dynamos denied Chennaiyin FC their sixth win in nine games this Indian Super League season.
The win gave three crucial points to Bengaluru FC, who are now leading the points table with 18 points from six wins in nine matches.
John Gregory has been penalised for making offensive remarks to the referee.
Sounding optimistic on the rapid development of Indian football and the growth of India as a football market, the 50-year-old Spanish CEO said he is "very positive on Indian football."
Thiago Santos rescued a point for Mumbai City FC with a 71st minute strike against hosts Jamshedpur FC as the two teams settled for an entertaining 2-2 draw in an Indian Super League encounter on Friday.
FC Pune City top the table with 16 points from nine matches, while Kerala are in 8th position with eight points after as many matches.
Pune have now moved to the second spot with 15 points from eight matches and are just a point behind league leaders Chennaiyin FC.
It looked like both teams would cancel each other out until the 72nd minute when Marcelinho threaded a pass forward for Emiliano Alfaro, who clinically buried it past Laxmikant Kattimani. Alfaro had a chance to double the lead two minutes later but his shot didn't have enough pace and was cleared away.
CK Vineeth's stoppage time goal earned Kerala Blasters a draw against Chennaiyin FC.
Brazilian Matheus Trindade Goncalves sent Bengaluru goalkeeper in the wrong direction in the first minute of the stoppage time to score the only goal.