Gong Oh-kyun’s side finished second with five points, two behind group winners Republic of Korea, who saw off Thailand 1-0 in the simultaneous kick-off.
As the Group C runners-up, Vietnam will face the Group D winners in the last eight.
Vietnam headed into the match Lokomotiv Stadium knowing that a win against Malaysia would be a must to keep their hopes alive.
The 2018 runners-up put up the pressure from the first whistle and threatened the Malaysian twice in a row with a Nham Manh Dung strike being denied by goalkeeper Firdaus in the 26th minute and Dung Quang Nho going over the bar shortly later.
Vietnam’s stormy attacks paid off in the 28th minute when Nham Manh Dung rose high to head home Nguyen Thanh Nhan’s cross to open the scoring.
Just before half-time, Malaysia’s hope for comeback was dealt a big blow when a VAR review led to Hairiey Hakim not only being penalised for a handball in the area but also red-carded for the offence.
Bui Hoang Viet Anh’s spot kick was saved by Firdaus but the Vietnamese defender quickly slotted home the rebound to make it 2-0.
Vietnam maintained their dominance in the second half and created several opportunities to widen their advantage. However, they could not capitalise on any of them to add a third goal.
Meanwhile, the Malaysians also failed to find the back of the net and exited the competition with their third successive defeat./.