The result means that home nation Singapore have to beat Indonesia on Thursday to qualify for the semi-finals. A draw will send Indonesia through.
A brace by Evan Dimas Darmono in the 4th and 13th minutes put the Indonesians 2-0 up and thereafter were always in control of the match.
During the second half they had several decent chances to increase their lead but poor finishing and some good defending stopped them from adding to the score line.
In the end Indonesia were deserved winners.
In the group standings Myanmar are top with 9 points from three games, followed by Indonesia and Singapore with six points. Cambodia are next with three points followed by the Philippines with zero.
The two remaining matches in Group A are between Myanmar and Cambodia on June 10 and in the last match on June 11, Singapore are up against Indonesia.