NorthEast had gone six matches without a win, losing four of them.
With just two points from their last six matches they were on the verge of exit until Ivory Coast midfielder Romaric scored from a stunning free-kick in the 81st minute here at the Indira Gandhi Athletic Stadium.
The victory helped NorthEast accumulate 14 points from 11 matches and move to the sixth spot. With three matches still left to be played their coach Nelo Vingada will feel confident.
Pune now have 15 points from 12 matches and will have to win their next two games to be assured of a place in the play-offs.
The battle was a cagey affair particularly in the first session when neither team enjoyed clear cut chances.
Pune's Momar Ndoye was the only player who got a sighter at goal but could not beat goalkeeper Subrata Paul from a narrow angle.
Pune's midfielder Jonatan Lucca also missed a good chance from just outside the box when the ball fell for him nicely but he could only shoot waywardly with his left-foot.
For NorthEast, there was hardly any chance of note with midfielder Katsumi Yusa's attempt on goal which goalkeeper Edel Bete saved without much difficulty. It was their only shot on target in the first half.
In the second session, Pune came out all guns blazing and were unlucky not to take the lead.
In the 69th minute, Lenny Rodrigues' fierce shot from 35 yards beat goalkeeper Paul but bounced off the crossbar.
Spanish midfielder Pitu then tried his luck after Izumi Arata had chested the ball down for him inside the penalty box but goalkeeper Paul measured up to the challenge with a one-handed reflex save.
Surviving the onslaught, NorthEast scored the match in the 81st minute.
The hosts won a free-kick just outside the box and Romaric stepped up to take it. The Ivory Cost midfielder used his left foot to devastating effect as his curling free-kick found the top corner of the net, past a diving Edel Bete.