Xuan Son added to his side's 2-0 first-leg lead in the 62nd minute with a close-range strike after Malaysia goalkeeper Azri Ghani had repeatedly frustrated the home team.
Xuan Son then put the result beyond any doubt in the 89th minute when he burst down the left flank before cutting inside and firing a low shot through Azri's legs that flew into the far corner of the net.
Vietnam, who are attempting to win back-to-back titles for the first time, will play seven-time champions Thailand in the two-legged final in a re-run of the previous decider at the end of the 2024 championship.
The Thais will host the first leg in Bangkok on Saturday with the return in Hanoi four days later.
