After a barren opening session, Churchill scored through Bineesh Balan (58th) and Sunil Chhetri (63rd) while Pune FC pulled one back through substitute Boima Karpeh (90th).
With today's win, Churchill are now on 45 points and a five-point lead at the top of the table with four matches left to be played.
Pune FC, who were also nursing title ambitions, were left to ponder on their defensive frailties as both goals they conceded resulted from mistakes at the backline.
Sunil Chhetri then fed Henri but the Gabonese striker delayed, allowing a rival defender to dispossess him.
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Pune FC did not have any clear chances in the first session with James Moga left stranded.
Much of the blame for Churchill's lead should be laid on goalkeeper Shahinlal Meloly whose poor goal-kick saw Henri trap the ball and lay it for substitute Bineesh Balan who showed remarkable poise to finish from a narrow angle in the 57th minute.
Just at the stroke of regulation time, Boima Karpeh pulled one back for Pune FC, providing for a nervy five minutes in the end.