The Federation Cup champions finished with 14 points to top group H as they earned the right to host the prequarterfinal, which will be against the group F runners-up.
The Vietnamese Cup winners, who needed a draw to qualify, were thus eliminated as Malaysia's Selangor advanced to the last 16 with a 3-2 win over Tampines Rovers.
Playing with a youthful side in absence of striker Nguyen Rogerio (suspension) and several regulars down with injury, the Vietnamese struggled to come to terms after conceding a penalty early into the match.
After the changeover, Penn Orji struck back to back in the 53rd and 59th minutes to give a commanding 4-0 lead.
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Two minutes later, Sai Gon Xuan Thanh pulled one back through Christian Jose Nsi Amougou but it was too late as the resolute East Bengal defence held on to their lead to continue their spectacular run in the AFC Cup.
This was for the second time the red and gold qualified for the AFC Cup knockout after their run in 2004.