The match began at a high tempo at My Dinh National Stadium, but Vietnam suffered an early setback when Van Vi was forced off injured in the 10th minute and replaced by Phan Tuan Tai.
Thailand took advantage two minutes later when Yotsakorn Burapha fired a low shot from outside the penalty area past goalkeeper Le Giang Patrik to put the visitors ahead.
Vietnam struggled to find an equaliser, although Xuan Son came close in the 43rd minute when his header from Tuan Tai's cross struck the crossbar.
Thailand were awarded a penalty two minutes into the second half after Xuan Manh fouled Kakana in the box, but the Thai number seven sent his spot kick over the bar.
Vietnam levelled in the 52nd minute when Tuan Tai crossed from the left and Hoang Hen's effort hit the post before rebounding off goalkeeper Chatchai and into the net.
The hosts continued to press, with Hai Long striking the post in the 69th minute before Quang Hai failed to convert the rebound.
Thailand regained the lead in the 85th minute after Tien Anh failed to clear the ball, allowing Wanchai to score from close range.
Vietnam responded deep into stoppage time. Tuan Tai crossed for Xuan Son following a quick counter-attack, and Wanchai, attempting to clear, turned the ball into his own net in the 93rd minute to make it 2-2.
The late own goal ended Thailand's hopes of overturning the first-leg deficit and secured Vietnam a 4-2 aggregate victory and a successful defence of their ASEAN Cup title.
