Marsela Awi beat the Vietnamese goalkeeper with a shot from outside the penalty box in the 38th minute before Ngoc Minh Chuyen earned an equalizer in the extra time.
Despite playing better than the home team, U18 Vietnam had to wait until the 72nd minute to find joy. From a corner kick, Nhu Quynh hit an accurate shot to make it 2-1.
For the rest of the game, Indonesian players did not create any significant opportunities and they finally conceded a 1-2 defeat.
Vietnam who crushed Singapore 9-0 in their opener two days ago now jumped to the top of Group A, with six points.
In another Group A match on July 26, Thailand stunned Singapore 6-0 to maintain their second place after two wins.
Singapore were eliminated from the tournament after their three consecutive losses.