Syed Rahim Nabi (7th) gave Bagan an early lead while Odafa Okolie (47th), who returned after recovering from fever, completed the tally to hand the Goan heavyweights a fourth successive defeat.
Peter Carvalho pulled one back for Dempo SC in the 51st minute to add to the excitement in the second session but they could not add to the tally.
Now Bagan have 13 points from 18 matches while Dempo remained on 35 points after 22 rounds.
Nabi's spectacular finishing set the tone of the action and Bagan continued a long session of dominance against the most successful team in the NFL/I-League history.
Bagan had three more chances to bolster their lead in the first-half but the second goal remained elusive as Dempo goalkeeper Laxmikant Kattimani denied two efforts from Odafa.
Dempo had one opportunity through Carvalho in the 26th minute but his long-range attempt went over.
Odafa, who was unlucky thrice in the first-half, made no mistake when Nabi set him up clear off the Dempo defence.
Dempo striker John Menyongar found Bagan upright on his 49th minute attempt before Carvalho reduced the margin as he headed home a measured cross from Anthony Pereira.
Dempo had a few more chances to find the equaliser but both Menyonger and Koko Sakibo could not find the right touch to beat Shilton Paul in the Mariners' goal.
The three most notable triumvirate in the Bagan attack - Nabi, Tolgay Ozbey and Odafa - came together to threaten the Dempo goal in the 53rd minute but a third goal eluded them.
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