Ranti Martins injected life into an otherwise dull start with a 12th minute goal from a rebound to put the Shillong outfit ahead.
The local challengers upped the tempo and levelled through substitute Taro Hasegawa in the 33rd minute before Luciano Sabrosa sealed the issue firing a 64th minute spotkick to register Mohammedan Sporting's only second win in 11 matches.
The win pushed Mohammedan Sporting (21 from 22 matches) one place up leaving Churchill Brothers (19 from 20) at the bottom even as they are not yet spared from the relegation threat.
They will now return to Shillong for the local derby on April 21 concluding match and a win too may not ensure safety as they have to take other results into count.
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David Ngahite who played up front with Ranti initiated the much important move when he beat Dhanarjan from the right and crossed it to Lalnunpuia at the far post.
Mohammedan Sporting custodian Luis Barretto thwarted the effort but Ranti showed great poaching skills scoring from the rebound.
Hasegawa cut in from the left before unleashing a powerful shot to bring up the equaliser.
Mohammedan Sporting could have taken a 41st minute lead after a fine work by Hasegawa and give Penn another chance, but the Nigerian continued his miserable day with another miss.
After break, the Sanjoy Sen side played with more intent as heat began to take toll on the Shillong side.