The match was heading for a draw with Arata Izumi's goal in the 23rd minute for Pune FC cancelled out by Nima Tamang in the 63rd minute.
Moga, who was kept quiet throughout the match by United Sikkim defence, ran past his marker to glance an in-swinging free kick from captain Douhou Pierre into the opponent's net in the second minute of the added time.
Pune FC thus avenged their 2-2 result in the first-leg home game. The win stretched Pune FC's unbeaten run to eight, while the win was sixth in away games and ninth in the league.
The victory took Pune FC to the top of the league table level on points with Churchill Brothers with a tally of 28 each. But since the Goan club had beaten them in the first leg encounter, head-to-head record keeps them on the top.
Pierre, adjudged the Man of the Match, had played a huge role in the first goal. His intelligent through ball was perfectly met by Izumi who calmly lobbed the ball over the onrushing United Sikkim goalkeeper Yoon Tae.
After conceding the lead, United Sikkim took charge of the game and created several opportunities but was let down by poor finishing. Nurudeen Salau had a great opportunity to level scores in the 25th minute but a tame shot from close range after receiving a ball from Nima did not help.
The equaliser for United Sikkim had a huge slice of luck. Nima Tamang's shot crashed into a couple of defenders and rolled past a helpless Pune FC custodian Abhra Mondal and into the net.
Star striker Jeje Lalpekhlua, nursing an injury, was introduced in the 57th minute but lasted just five minutes. His injury flared up again and was replaced by Khanthang Paite.
With this loss, United Sikkim are under tremendous pressure as the Gangtok based club is languishing in relegation zone with nine points from 13 matches.
