It was Timor-Leste who had a golden opportunity to open the scoring after just three minutes after Marc Klok conceded a penalty with a rash lunging challenge, but Ernando Ari came to Indonesia's rescue by denying Mouzinho from 12 yards.
With that reprieve, the Indonesians would go on to break the deadlock in the 16th minute when a high ball was floated up to the far post and headed back into the six-yard box by Rizky Ridho, paving the way for Egy Maulana to tap home from close range.
Seven minutes after halftime, Witan Sulaeman doubled Indonesia's lead when he was unchallenged inside the area after a long throw somehow sailed over a sea of players, allowing the midfielder to divert a header into the back of the net while literally standing still.
The Indonesians then effectively but the result to bed when Fachrudin Aryanto added a third in the 58th minute, although Mouzinho made amends for his earlier failure from the spot by pulling one back 11 minutes later after he got in behind the opposition defence and rounded Ernando to score.
But with 13 minutes remaining, Witan grabbed his second of the evening with a clinical left-footed strike into the bottom corner after his late run into the box was picked out by a cutback from the left wing, wrapping up a much-needed win for Indonesia.
It took Myanmar just two minutes to open the scoring when Htet Phyo Wai did well to hold off a challenge before playing a slide-rule pass to release Win Naing Tun, who calmly slotted through the legs of the onrushing Quincy Kammeraad.
Four minutes after the half-hour mark, Philippines equalised when opposition goalkeeper Pyae Phyo Thu needlessly rushed out of his goal but flapped at a corner -- allowing Christian Rontini to help the ball on for Jovin Bedic to nod into the unguarded net from less than a yard out.
Bedic then struck three minutes later when he sent Pyae Phyo Thu the wrong way from the penalty spot after Oliver Bias had been felled inside the area, but it was then Myanmar's turn to hit back in the 51st minute when an enterprising run down the right by Win Naing Tun eventually saw him float a cross that was deftly headed into the bottom corner by Lwin Moe Aung.
With the tie now evenly poised, it was Myanmar who would go on to find the winner just two minutes later when a corner hung up at the back post was nodded back across goal by Lwin Moe Aung, and it was Soe Moe Kyaw who showed great determination to get in ahead of Kammeraad and stab a shot home from close range.
Tuesday's results mean that it is Myanmar who are currently top of Group A on six points, two ahead of Philippines and Vietnam with Indonesia a further point adrift, while Timor-Leste have been eliminated with a game to spare following three straight losses.