Mac Hong Quan, Vo Huy Toan and substitute Nguyen Van Toan pitched in with a goal each.
Vietnam have grabbled six points from two wins, having beaten Brunei 6-0 in the group's curtain-raiser.
Theconvincing win on June 2 gives Vietnam and an advantage in the group,which includes Thailand, Laos, Brunei, Malaysia and East Timor.
Vietnam'sU23 squad began their second game with an attacking style, but it wasMalaysia who got the first shot at the goal in just six minutes.Defender Salamat's free kick found Vietnamese goalkeeper Nguyen MinhLong well positioned to collect it.
Vo Huy Toan netted the ball in the 12 minute, but was adjudged offside.
Phuong set up a clear chance for Vietnam in the 14 when he was illegally tackled by a Malaysian defender in the penalty box.
Quan made no mistake from the spot to open the score for Vietnam.
Malaysia launched counter-attacks to try and tie the game, but they failed to penetrate a solid defence mounted by Vietnam.
A goal from Malaysia in the 37th minute was also called off-side.
Inthe 44th minute, Malaysia striker Abu Hassan Saari pouched the ballfrom a Vietnamese defender to face the goal, but his shot was not goodenough to beat Long.
During injury time in the first half, VanNgoc combined well with Phuong in a rapid counter-attack to help Vietnamleave the first half with a 2-0 lead.
Just two minutes from thebreak, Vietnam were awarded a penalty kick after Phuong was tackled by aMalaysian defender in the 18-yard area.
Vo Huy Toan made it 3-0 from the spot.
Forhis brace, Phuong scored the best goal of the match, curving a 25m freekick to the high corner of Malaysia's net past leaping custodian MohdFarhar.
Substitute Syahrul Azuwari Ibrahim pulled back a goal for Malaysia in the 78th minute, but in the very next minute.
Vietnamesesubstitute Nguyen Van Toan completed a convincing win for Vietnam,evading an offside trap to lob the ball to the net in the 79th minute.-VNA