Vu Duc Tung opened the scoreboard for Vietnam in the first half but Khairul levelled the score for Malaysia in the 36th minute.
With a sudden strike, Awalluddin of Malaysia secured the match-winner with just two and a half seconds left on the clock.
The win was Malaysia's second over Vietnam following a 5-1 victory in the semi-finals of the AFF Championship in Ho Chi Minh City last November.
The Vietnamese team is scheduled to face Bahrain in the second match of Group A on February 3.
VNA/VNP