Kerala needed just a point to qualify for the semi-finals while NorthEast United would have gone if they had collected all the three points. But Kerala did not disappoint the massive 53,000-plus home crowd present at the Jawaharlal Nehru Stadium with Vineeth scoring the all-important goal.
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-leg semi-final battle. League toppers Mumbai City FC will face Atletico de Kolkata in the other semi-final.
With the loss, Northeast ended at fifth with 18 points from 14 matches.
Both teams started nervously trying to gauge each other's strengths but it were Kerala who were in command and could have surged ahead in the third minute.
Haitian international Duckens Nazon got the ball down on the left, cut past Mailson Alves and found space inside the box. However, his attempt on goal was palmed away by NorthEast goalkeeper T P Rehenesh.
Apart from that early goal-mouth action, there was not much that either team did to break the deadlock. Most of the chances came from set-pieces but the teams could not get it right. Two free-kicks of Kerala on top of the box were wasted.
In the second session, NorthEast showed more urgency. Emiliano Alfaro's effort from just inside the box saw goalkeeper Graham Stack prove equal to the challenge in the 60th minute.
The game got its decisive moment in the 66th minute. Mohammed Rafi switched play and found Vineeth on the left. The winger did well to cut inside, switch the ball to his right foot and take an unexpected grounder which beat the rival goalkeeper.
The goal stunned NorthEast as they suddenly appeared to lose hope, despite coach Nelo Vingada ringing in the changes. They now had to score two goals to turn the match in their favour, although it were Kerala who seemed more likely to score again.
Kervens Belfort saw his attempt go straight into the hands of NorthEast goalkeeper Rehenesh two minutes after taking the lead. In the 75th minute, substitute Antonio German brought the best out of Rehenesh who kept his team alive with a diving save.
Rehenesh's best save of the day came three minutes before the end when he palmed Rafi's header from point-blank range on to the post. It counted for nothing in the end as Kerala sailed home and now have the chance to seal their second final appearance in three years.