The win has strengthened the Vietnamese squad's chances of entering the final round, which will see 10 group winners and five second-placed teams from all groups, who will join hosts Qatar at the AFC U23 Championship 2016.
The January 16, 2016 team competition would also serve as Asia's qualifying tournament for the Summer Olympics to be held in Rio de Janeiro next year.
Malaysia's Captain Nazirul Naimche Hashim opened the scorecard in the 35th minute of the match, which saw the visiting side play on the offensive from the beginning.
His free kick from a distance of 35m touched the crossbar and entered the net, where Vietnamese goalie Hoai Anh was too startled to do his job.
This was the second time that the ball hit the crossbar. During the 20th minute, Vietnamese midfielder Pham Manh Hung nearly scored the first goal of the match when his free kick swung out of the goalkeeper Mohd Farhan's reach, but could not overcome the bar.
The player, who has been asked to train hard with free kicks, also tested Farhan for the second time during the concluding moments of the game, but his shot hit the bar again.
Just three minutes after the opener, Vo Huy Toan levelled the score for Viet Nam with a magnificent shot straight into the net.
Striker Nguyen Cong Phuong received the ball near the box. He managed to move to the right before heeling Toan, who ran fast and aimed a canon shot at goalkeeper Farhan.
"I was really happy to score a goal during my comeback match in this stadium (after the first time three months ago during the AFF Cup). It was more special as my goal played a role in Viet Nam's victory today," Toan said during an interview with the K+ channel after the match.
SHB Da Nang FC's striker suffered an injury and left the field earlier-than-expected. But he said he would be okay for the next game.
Towards the end of the first half, many in the audience thought the match would end in a 1-1 draw. But it was Phuong who made a difference.
He grabbed a goal for himself after tapping a perfect long free kick from Viet Nam side.
The famous player broke the offside trap and made an easy job of the 2-1 score for his side.
In an earlier match of the group, Japan began their campaign with a bang as they whipped Macau 7-0 at the Shah Alam Stadium.
The Japanese were ahead 4-0 during the break and added three more goals after the interval, including two during stoppage time, in the Group I opener.
Sanfrecce Hiroshima player Gakuto Notsuda scored a double (31st, 90+2th) with Skipper Wataru Endo (22nd), Suzuki Musashi (66th), Yuta Toyokawa (26th) and substitute Takumi Minamino (90+3th) also added to the score sheet for Makoto Teguramori's side.
Buoyed by their massive opening success, Japan will be aiming for a second consecutive win when they play against Viet Nam, while Macau will seek their first victory as they face hosts Malaysia tomorrow.
VNS