Churchill Brothers, who led 2-1 at half time, scored through Anthony Wolfe (16th), Raju Yumnam (26th) and substitute Balwant Singh (90+1).
Home United pulled one back through Qui Li (10th).
At the end of third round, Churchill Brothers have collected six points from three matches. While Home United, who are yet to win, have one point from three games.
The win gives Churchill Brothers a big boost ahead of their away match on April 2.
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The visitors surged ahead on the 10th minute though Qiu Li, who beat keeper Lalit Thapa off a back pass from Ahmed Fahmia Bin Jamil.
Unnerved by the setback, Chuchill Brothers kept on probing into the rival box and found the equaliser six minutes later.
Thangjam Saran Singh, from the left, crossed the ball into the box for unmarked Anthony Wolfe who made no mistake in heading the ball into the net.
After the change of ends, both the teams made a change with the visitors holding an edge and had a chance to find the equaliser, but Lalit Thapa made a brilliant save from five yards to deny Famie.
With both the teams going for the kill in the last quarter, it was substitute Balwant Singh who sealed the issue in Churchill Brothers' favour. He collected a pass inside the box, beat three defenders before getting past Shanril.