The win was Malaysia's second in as many matches and gave the team six points to head the table of four teams with six points while Thailand in second place has four points against third placed Myanmar's one.
However, the win did not come easy as Myanmar were piling on the pressure early in the match and even took the lead in the first half through Nay Lin Tun who scored in the 38th minute.
When the second half started, coach Ong Kim Swee's pep talk seemed to have worked its magic as his boys were full of running and kept the pressure on before the Myanmar defence wilted.
Skipper Mohd Irfan Fazail equalised in the 64th minute when he finished off a move started by Putera Nadher to give the 2,000 odd fans some reason to cheer.
Boosted by the equaliser, Kim Swee's boys showed better coordination, especially along the flanks with A. Thamil Arasu and D. Saarvindran causing all sorts of problems along the flanks.
Malaysia though had to wait until the 78th minute to ensure all three points but it was worth the wait as Wan Zack Haikal struck a superb free-kick into the top corner to ensure victory.
Malaysia will complete their fixture against Thailand on Wednesday.
Despite the win, Kim Swee kept his emotion in check but admitted that he was pleased with the performance of his boys but would only be satisfied by winning the title.
"I will be even happier if we can bring back the gold medal from the Myanmar SEA Games," he said.