The hosts only needed 20 minutes to open the scoring courtesy of a strike from Tran Danh Trung. Nguyen Huu Thang’s follow-up five minutes later extended the lead to 2-0.
Malaysia drew equal during the second half with goals from Aliff Haiqal and Wan Ar san.
But in the final minute of the match, Bui Minh Duc’s score sealed the victory for the Vietnamese team.
Vietnam 1 team will now face Indonesia in the afternoon of October 5.
In group B, Vietnam 2—the U13 Song Lam Nghe An team—lost their October 4 match against Thailand 0-2.