Lalram Chullova's 21st-minute penalty strike for the recently crowned I-League champions was cancelled out by Ghanefo Kromah's 84th-minute goal from the spot as well.
But Laldanmawia Ralte's 89th-minute header settled the tie in Aizawl FC's favour in the Group A match.
It was a slow start to the game with both teams playing with caution and the only real action in the first 15 minutes was a Kamo shot.
The match came to life in the 21st minute when Aizawl FC were awarded a penalty after Lalruatthra was brought down by Adil Khan inside the box, prompting the referee to point to the spot.
Albino Gomes, on the opposite end, kept out Brandon Fernandes' shot a minute later as the Goan outfit searched for the equaliser.
Syrian import Mahmoud Al-Amna formed a trio with Jayesh Rane and Bayi Kamo upfront and his presence and ability to take the ball into the final third gave Churchill defence a tough time.
It was not long for Churchill to test Aizawl FC's defence, but the Mizoram side's centre-back pairing held up to the task. Churchill enjoyed healthy spells of possession in the final third in the second half but could not make anything out of it.
In the 72nd minute Kromah latched onto a long ball and almost released his shot but was shrugged off by the Aizawl FC defence line.
Churchill were awarded a penalty in the 84th minute and Kromah stepped up to score with confidence to make the scoreline 1-1.
But Ralte spoiled Churchill's party as his header in the 89th minute found the back of the net to give Aizawl the full three points.
Disclaimer: No Business Standard Journalist was involved in creation of this content
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