The match at Jalan Besar Stadium saw little action from Vietnam until the 84th minute, when Nguyen Xuan Son unleashed a stunning volley into the top corner after controlling the ball with his back to the goal.
However, after over five minutes of reviewing the play on VAR, the referee disallowed the goal, ruling that the ball had touched Son's arm.
The decision sparked strong reactions from Vietnam players and coaching staff, with head coach Kim Sang-sik receiving a yellow card from South Korean referee Kim Woo-sung.
Despite the setback, Son's brilliant moment brought new confidence to the team.
In the eighth minute of injury time, Tien Linh made a cross from the left wing, leading to a defensive mix-up between Singapore's goalkeeper and a defender, who collided and let the ball loose. Son (number 12) was there to retrieve it, prompting defender Shakir Hamzah to block the ball with his hand.
The referee pointed to the penalty spot without hesitation.
Tien Linh stepped up and calmly slotted the penalty into the left corner as goalkeeper Izwan Mahbud dived the wrong way, breaking the deadlock in the 11th minute of injury time.
The goal was Vietnam's ninth finishing attempt in the match.
Linh moved to second in the tournament's top scorers list with three goals. After netting, the 27-year-old striker celebrated with his trademark finger-to-lips gesture as a way to response to the home crowd, who have been putting pressure on Vietnam players constantly throughout the game.
With the momentum, Vietnam went for another goal. In the 13th minute of injury time, Nguyen Hoang Duc's corner kick found Pham Xuan Manh, who delivered a quick pass into the box.
Son moved forward and tapped the ball into the net, sealing Vietnam’s 2-0 victory.
Son proved himself as one of the most efficient scorers in the tournament, averaging a goal every 60 minutes.
Alongside Linh, Son now shares the second spot on the top scoring list with three goals each, just behind Singapore's Shawal Anuar, who is leading with four.
This was the fifth consecutive match in the tournament that Vietnam failed to score in the first half. Like their group stage game against the Philippines, the team struggled to dominate on artificial turf but found the goals in the dying minutes.
The late goals give Vietnam a huge advantage before the second leg at home on Sunday.
