Beikhokhei (5th and 40th minute) and Robin Singh (66th and 90+3) scored two goals each while India captain Sunil Chhetri found the target in the 33rd minute.
Boima Karpeh (74th), Beevan Mello (89th) and Victorino (90+1) scored for Sporting Clube de Goa in the Group B match at MDSC Stadium at Manjeri.
The late goals from Mello and Fernandes gave Bengaluru FC some headache after Boima had pulled one back for the Goan side who were down by four goals till the 73rd minute.
Robin scored in the second half before Sporting's mini-comeback to add to Bengaluru FC's three goal cushion in the first session.
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Boima, who scored one and set up the other two for Sporting, missed a penalty in the 58th minute.
Earlier, John Meyongar floated the ball into the area with Sean Rooney chasing it. Sporting goalkeeper Ravi Kumar fluffed with the ball falling nicely for Beikhokhei who slammed the ball into the back of the net.
Beikhokhei notched up his second seven minutes later to underline Bengaluru's domination in the first half. Chhetri turned provider twisting and turning his marker to set up Beikhokhei who just had to tap in from close range.