Willis Plaza (30') opened the scoring in the first half for the Red Machines. Cameroonian striker Aser Pierrick Dipanda (45+3' [Pen.] and 70') scored from the spot just before the half-time whistle and added in another in the second half to see the Green and Maroons through.
Churchill, who earlier got relegated from the I-League after finishing ninth had won their Super Cup qualifier 2-1 over Indian Super League (ISL) side Delhi Dynamos and carried over that form as they dominated proceedings early on.
Nicholas Fernandes ran down the middle of the pitch and fed the ball for Willis Plaza on the edge of the opposing box. The Trinidadian took a touch, went past defender Eze Kingsley Obumneme and found the back of the net past Shilton Paul to add to his two goals against Dynamos in the qualifier.
There seemed to be no answers from the other end until Churchill gifted a cheap penalty in the first half injury time. Nicholas Fernandes' mistimed tackle brought down Sheikh Faiaz in the box and Dipanda stepped up.
I-League 2017/18's Golden Boot winner drove the ball straight down goalkeeper Ricardo Cardozo but he fumbled and Dipanda slotted the loose ball to make it 1-1 at the break.
Churchill defender Monday Osagie had to be substituted at the hour mark and that made it a bit easier for the Mariners. A rejuvenated Bagan had both Akram Moghrabi and Dipanda trying hard to put their team into the lead.
The eventual winner did arrive from a set-piece nonetheless. Cameron Watson's freekick from his own half carried through to the box and the lanky Moghrabi leapt the highest to head the ball down. Dipanda, at the right place, drove a left-footed shot that went into the bottom left corner of Cardozo's goal.
With twenty minutes remaining, both sets of forwards tried their luck at either end. It must be noted that Plaza and Francis came close to scoring an equaliser.