Gabonese recruit Henry Antchouet scored both the goals (19th, 35th) as the Goans' resolute defence denied the local giants any chance to come back in the second half.
The win took Churchill Brothers (51) eight points clear of the second-placed team and they now need a draw from their remaining two matches (Air India and Mohun Bagan) to win the title for the second time after their triumph in 2008-09.
East Bengal and Pune FC, both on 43 points, lie on second and third places on goal difference as they have three games each.
Playing without their ace midfielder Roberto Silva, Churchill Brothers did not have any problem up front with Henry and Sunil Chhetri forming a fine combination.
Henry gave them the lead from a square pass off Chhetri, while he completed his second from a solo run.
Technical director Subhas Bhowmick's tactical acumen ensured Mohun Bagan's prolific striking duo of Odafa Okolie and Tolgay Ozbey had an off day.
A frurstrated Odafa was also unlucky with his curling leftfooter hitting the bar in the first half, while Churchill goalkeeper Sandip Nandy did a neat work under the bar.
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