Pune City lost 0-4 against Goa in their penultimate clash but their impressive performances earlier in the season means they don't have to wait for the final league clash to secure a point for a place in the play-offs.
Zequinha was the star of the show, striking in the 73rd minute to give his side the lead and the winner.
Pune have now moved to the second spot with 15 points from eight matches and are just a point behind league leaders Chennaiyin FC.
Balwant scored on either side of half-time to ensure a 2-0 win for the Mumbai outfit.
NorthEast United were dealt with a huge blow when their goalkeeper TP Rehenesh was sent off for a last-ditch tackle on Mark Sifneos.
The 47th minute strike was enough for the in-form table toppers to finish the game with three points at the Indira Gandhi Athletic Stadium.
This was Dynamos' second consecutive loss after their 1-4 thrashing by Bengaluru FC on November 26. They now have just three points from three matches.
Chennaiyin FC beat NorthEast United 3-0 in the match in Chennai on Thursday.
Chennai registered their first win at home over NorthEast United in the ISL and only their second victory over their North-East rivals.
NorthEast could have got their opening goal as early as in third minute, but Marcinho fluffed a very easy chance when he hit on high after being on a one on one with goalkeeper Subrata Paul.
The Indian Super League coaches said that the new six Indian player rule will help the local players develop their game.
ISL franchise NorthEast United FC owner John Abraham said his team will break-even within next one or two seasons and will become the first one among all the teams.
The win helped Kerala finish second in the league table with 22 points from 14 matches, and will now meet third-placed Delhi Dynamos in the two-legged semifinals
The win took NorthEast United's points tally to 18 with a match in hand, but they still continue to be placed fifth and will need to beat Kerala Blasters in their final league game to reach the semis
Shouvik Ghosh headed the ball in off a corner kick in a dramatic fashion with just seconds left in the match to hand NorthEast United a dramatic 3-3 draw vs Chennaiyin FC
Romaric gave NorthEast United FC a 1-0 win over FC Pune City to keep their hopes of qualifying for the Indian Super League knockouts alive.
Iain Hume's last-gasp goal helped Atletico de Kolkata secure a point vs NorthEast United, meanintg they remain in the top four with 14 points from 10 matches