Willis Plaza's early strike was not enough as Hussein Eldor's own goal (43') and Ansumana Kromah's 87th minute penalty sealed three points in favour of the hosts.
There were three changes in Aizwal's first 11 from the side that beat Shillong Lajong 4-1 on Monday. Lalawmpuia replaced Gurpreet Chabal in goal while Lalrinchhana aTochhwng and Lalkhawpuimawia (Mapuia) stepped in place of Mamit Vanlalduatsanga and Lalremsanga Fanai. Churchill coach Petr Gigui started with an unchanged 11 from their 3-2 win over Chennai City.
It took Plaza just five minutes to get on the scoresheet for the 21st time this season as he got the better of his marker in Richard Kassaga to bury Nicholas Fernandes' delivery from the left. The Trinidadian shot wide from another chance just minutes later.
Paul Ramfangzuava directed his header straight at Churchill goalkeeper Kunzang Bhutia from an Isak Vanlalruatfela cross from right before the half hour mark
Kromah got himself in promising positions quite a few times but wasn't able to do much with the ball inside the opponent's box.
Mapuia put the Churchill defense under enough pressure while vying to get on the end of Lalrinchhana's pass from the right which ended up in Eldor turning the ball into his own net in the 43rd minute as the teams started the second half 1-1.
Aizawl goalkeeper Lalawmpuia rushed off his line twice in the first 10 minutes of the second half, besides once more a bit later, to block Plaza from helping the visitors regain their lead.
Around the hour mark, it was Mapuia putting pressure on the Churchill backline once again after a delightful curling ball was played in by Lalrinfela but Bhutia got enough of an intervention to see the former's header go wide.
Before being taken off in the 76th minute, Mapuia forced a save off Bhutia after Kromah's shot at goal was blocked by Eldor in the 69th minute while Lalawmpuia kept his side in the game by keeping out Churchill subsitute Anthony Wolfe's attempt from inside the box in the 81st minute.
Aizawl confirmed their seventh place finish as Kromah made good use of the opportunity from the late penalty after Bhutia was deemed to have brought down the Liberian inside the Churchill box with referee Ajitkumar Meitei Lairenlakpam pointing towards the spot.