Pham Xuan Manh scored a double for the hosts in the first half while Joshua Bernard Pereira narrowed the result in the second.
The win strongly improved Vietnam's top position in the ranking with six points after two matches.
Vietnam had already qualified for the semi-finals after beating Thailand 2-0 in the first games some days ago.
Despite a loss, Singapore followed Vietnam to the knockout round as they are the second-placed squad. Singapore has one point along with Thailand after their draw but have a better goal difference.
A Vietnamese striker opened the score from a mistake of Singapore's goalkeeper Muhammad Zharfan Bin Rohaiza at the fifth minute.
Rohaiza, in an attempt to kick a ball away, missed it and Manh quickly stole the ball and successfully netted it.
Rohaiza's mistake was attributed to the heavy rain that strongly affected the grass field of the Thong Nhat Stadium.
About half an hour later the Vietnamese forward was again in a right place, receiving a long ball before passing Singapore defenders to make it 2-0.
Singapore, who had no opportunity in the first 45 minutes, created some attempts after the interval with some changes in their line up.
Pereira stole a ball from Vietnam's substitute Do Hung Dung about 5m in front of the box. He met no difficulty to convert the chance into a goal at the 75th minute mark.
In the semi-finals on November 26, Vietnam will play defending champions Hoang Anh Gia Lai who came from behind to beat Myanmar 4-3 in the late match of the day.
Hoang Anh Gia Lai, who always lure thousands of supporters to their matches, were given a heavy punch just seven minutes to the game.
Zaw Hein's shot hit the right pole but his teammate Yan Naing Oo ran in and did not give goalkeeper Pham Van Tien a second chance.
About 10 minutes later Hoang Anh Gia Lai leveled the score with a perfect header by Nguyen Cong Phuong, who will compete in Japan next year.
Mg Mg Lwin pushed his team ahead for the second time with a banana-shaped kick that went out of Tien's reach.
Goal hunter Nguyen Van Toan brought the game to a tie some minutes later. He broke the off-side trap before leaving goalie Phone Thitsar Min behind to shoot it in.
The second half of the game totally went to the defending champions as they set up strong domination and pocketed two more goals by substitutes Kim Hung and Tran Minh Vuong.
Myanmar captain Htike Htike Aung narrowed the result in the extra time from a free kick.
Goalie Tien dropped the wet ball which went straight to the net.
With the win, Hoang Anh Gia Lai stands second in the Group B with three points.
The top position belongs to the Republic of Korea's U19 squad who will play Singapore in the second semi-final match on November 27.