Antchouet scripted the win for the Churchill Brothers with strikes in the 34th and 45+2nd minutes, while super-sub Akram Moghrabi completed the tally in the 82nd minute as the Goans went four points clear of East Bengal at the top of the table.
Churchill have 37 points from 15 matches, compared to 33 of second-placed East Bengal who have played two matches more.
In the top of the table clash, Churchill did not give the local side any chance as the Gabonese recruit gave the lead from a Steven Dias assistance at the Yuba Bharati Krirangan.
Moments before the half-time whistle, Henry doubled the lead with Dias again instrumental in setting up with a sharp cross from right.
Moghrabi, who replaced Beto in the 79th minute, made his presence felt when he headed the ball home from a corner kick.
Churchill thus avenged their 0-3 loss in the first leg two months ago.
But since then, Churchill under technical director Subhas Bhowmick have remained unbeaten in nine matches, winning eight of them to charge up the ladder into pole position.