Edward Junior Wilson’s 10th goal of the AFC Cup campaign had seen Padang cancel out Ryuji Sueoka’s solitary goal from the first leg in Kolkata last week.
But with 12 minutes remaining at Agus Salim Stadium, first-half substitute Moga headed home to put East Bengal ahead 2-1 on aggregate.
Marcos Falopa’s side will play the first leg of their semi-final away from home next week.
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