The crucial goal came in for the host in the 61st minute when Isaac netted a pass from Brazilian Fabio Pena when the former's shot deflected off Arnab Mondal and past the keeper.
The home side with five U-22 players needed a win to stay in the I-League next season while the Red and Gold brigade from Kolkata finished third this season irrespective of their loss here.
The home side were on an attacking spree right from the first whistle but failed to convert on a number of attempts.
Bhutia misjudged a free kick from Dika that slipped off his grip only to find a defender to his rescue and headed it off to safety.
At the front, Ulliams Bomfin and Fabio Pena were busy keeping T P Rehenesh Singh and East Bengal defenders occupied, assisted by Penn Orji.
Returning after the break, the trio kept their 8000 fans at the grounds boisterous with their attacking spree before they were rewarded with the decider in the 61st minute.
The win also ensured Lajong's entry in this year's Federation Cup.
