The match, held in Nakhon Ratchasima city of Thailand, saw Vietnam score both goals in the second half.
The first goal found the back of the net at the 25th minute, followed by another at the 32nd minute, securing a dominant lead over Malaysia.
At 3:30 pm on November 5, the Vietnamese team will face Brunei in a decisive match that will determine their path to the semifinals.
In other Group B matches on November 4, Myanmar drew 3-3 with Australia, while Indonesia delivered a stunning 9-0 victory over Cambodia.