In a relegation six-pointer it was the Red Machines who took home all three points as the former world-cupper converted a spot-kick.
Thangjam Saran Singh made way for Costa Rican striker Cristian Lagos in the Mariano Dias' first eleven, while Santosh Kashyap handed Kim Song Yong, Steven Dias, Sushant Matthew and Rehenesh TP their debuts for Rangdajied United.
The away side started the match on the front foot and kept the pressure on the Federation Cup champions initially. In the 15th minute, the visitors found the back of the net when Edmar Figueira toe-poked a delightful through pass by Kim Song Yong, but the Brazilian was already flagged for offside.
Minutes later, Churchill's latest signing Cristian Lagos sent in a cross from the right to Alesh Sawant, however a well timed interception by rival goalkeeper Rehenesh TP averted the danger before Steven Dias' attempt narrowly missed the target at the other end at the half hour mark.
Lagos sent a scorcher of a left footed attempt crashing into the post from a Denzil Franco cross in the 41st minute as the two teams went into the break goalless.
It took 10 minutes in the second half for the home side to put themselves in the lead after Rehenesh was deemed guilty for a foul on Lagos inside the penalty area.
Anthony Wolfe stepped up to the spot to convert the resultant penalty, but not before the rival goalkeeper had blocked the former Trinidad and Tobago international's initial shot.
Churchill defender Ravanan Dharmaraj put in a solid block to deflect a dangerous cross from Steven Dias wide in the 70th minute while Balwant Singh missed an opportunity to make it 2-0 three minutes later in a one-on-one situation with Rehenesh.
Thapa came to the rescue once again in the 86th minute to keep out a shot from Yohei Iwasaki. That was before the Meghalayan team's skipper Eugeneson Lyngdoh almost saw his free-kick dip inside the left corner if not for the Churchill goalkeeper's diving save with 10 minutes to go.
With this win, the defending champions lift themselves off from the relegation zone and lie 11th with 13 points from 14 matches. Rangdajied now occupy the bottom spot with 12 points from 15 matches.
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