East Bengal and Minerva FC are both on 13 points after six matches but the red and gold brigade are on top by virtue of a better goal difference.
The I-League debutants came close to scoring on more than one occasion but Rafique took the wind out of their sails with a stunning 44th minute strike to ensire full points for the home team.
Mahmoud Al-Amna's corner was headed away by the Kerala defence but it went straight to an unmarked Rafique, who chested the ball down before firing it in with a drilling shot from outside the box as East Bengal won their fourth match on trot.
The Kerala outfit looked fine as a unit and impressed with their attacking skill barring the blot by Mirza, who was red-carded for his tackle on Katsumi Yusa.
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Such was Mirzas wild swing on Yusa that the star Japanese had to be stretchered off the field and replaced by Surabuddin Mollick in the 61st minute.
East Bengal had another chance from a free kick from Eduardo but his shot flew past the Gokulam Kerala crossbar late in the second-half.
It was the Kerala outfit, which dominated the proceedings in the first-half and came close to scoring on a couple occasions.
First East Bengal had a narrow escape in the 17th minute, when Ambane hit the woodwork from a Kamo Bayi free kick.
East Bengal attacked through Yusa on the left-flank but most of them either lacked power or were thwarted by the Kerala defence.
But before they could hold on to a clean slate East Bengal scored through Rafique from an Al Amna corner.
The Kerala outfit received a blow minutes after the kickoff when their Syrian midfielder Khaled Al-Saleh had to be replaced apparently after pulling his hamstring muscle.
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