Churchill, which needed a win to finish third, however, suffered a setback when they conceded a goal in the 18th minute when C S Sabeeth headed home a cross from Malsawmfela.
Stunned by the setback, Churchill Brothers regrouped and kept the pressure on their rivals and equalised in the 24th minute when Henri Autchouet found the net with a neat header off a cross from Mohammed Rafi to have both the team leading 1-1 at half time.
Changing over, Churchill continued in their pursuit of a win and took the lead in the 51st minute when Lalrindika Ralte headed in off a cross from Steven Dias from the right.
Eight minutes later Pailan conceded a penalty when defender Gurtej Singh brought down substitute Roberto Silva inside the box and referee CR Srikrishna awarded the penalty which was converted by Henri Autchouet to earn the ‘man of the match'.
The visitors matched their fancy rival put up a good fight and after coming close to scoring on a couple of occasions reduced the margin in the injury time through C S Sabeeth who headed in off a cross from Deepak Devrani.
Churchill Brothers who finished their league engagement with 48 points from 26 matches finished third. While Pailan Arrows remained on 13th position with 16 points from 26 matches.
Dempo who emerged champions for fifth time topped the table with 57 points followed by East Bengal (51 points).