Churchill rode on a Boima Karpeh goal in the injury time of second-half to beat Southern Samity, who finished second as both the teams made the last-four cut.
In the second match of the day, 27 times Shield champions East Bengal ended their campaign with a 3-1 win over China's Shandong Lueng FC, who finished with the wooden spoon in Group A.
Down 0-1, East Bengal scored through Baljit Singh Sahni (41st), R Vashum (77th) and Ravinder Singh (90+3rd) to make a spirited comeback.
The China outfit drew the first blood through a Mi-Hao-Ling goal in the 22nd minute.
Churchill finished with nine points, while Southern Samity had seven to be on second spot ahead of Mohammadan Sporting (5), East Bengal (4) and Shandong (3).