Churchill scored through a self goal by Abhishek Yadav (17th), Akram Moghrabi (33th) and Roberto Silva (62nd), while Mumbai FC, who lost their third successive match, reduced the margin through Yusif Yakubu in the 62nd minute.
Mumbai FC, having lost previous two outings, played with determination as they dominated for better part of the first session, but failed to score.
Veteran Yusif Yakubu, who played his first match, made few penetrating moves and had a chance to put his team ahead in the 7th minute but was late in connecting the ball off a free kick by Nicholas Rodrigues.
Few minutes later Subhas Chakraborty had a chance when he was found free inside the box but his right footer was put out by a diving Churchill keeper Sandip Nady.
Churchill Brothers, who played enterprising football against ONGC, looked a completely different side as they failed to combine themselves in the midfield and committed lot of errors, with rivals penetrating their citadel more often.
However, they managed to forge ahead against the run of play as defender Abhishek Yadav conceded own goal when he directed his shot into his own goal while clearing a low cross from the right by Denzil Franco in the 17th minute.
Akram Moghrabi, who scored a hat-trick in the previous match, doubled the lead when he found the net with a clinical header off Steven Dias flag kick from the right in the 38th.
Mumbai suffered a setback in the 38th minute when defender Evans Quao was red carded by referee Ajit Metei for bringing down Akram Mogharabi inside the box.
Mumbai FC tried to come back into the match in the second half when they reduced the margin in the 62nd minute as Yusif Yakubu scored off a header after he was fed by Dane Pereira off Subhas Chakraborty, but their challenge ended when Roberto Silva scored off a penalty.
Silva, who was unlucky when his diving header hit the post off Denzil Franco cross earlier, converted a penalty in 68th minute after Raju Yuminam was brought down by Subhas Chakraborty.
