After a barren first half, Shillong Lajong scored both the goals in the second half through Man of the Match Boithang Haokip (55th minute) and Cornell Glen (69th) at the Nehru Stadium.
The win takes Lajong to six points from as many matches.
While Dempo, who suffered their first defeat, remained on seven points from six games.
Sitting at the bottom half of the table, both the teams were looking for a win to move up the ladder. Shillong Lajong created more chances but lacked finishing touches.
Shillong Lajong too needed a win badly after losing four matches, and played with all their four foreigners for the first time with Uilliams Silvs, Penn Orji and Cornell Gen combining well to trouble the rival defence.