Vietnam were third with 73 golds while Indonesia, who won a massive 182 golds when they hosted the 2011 Games, finished fourth with 65 titles.
It is the 12th time that Thailand have been crowned overall champions since the biennial event was launched as the Southeast Asian Peninsular (SEAP) Games in 1959.
With more than 700 participants, Thailand were also the best in international sports, winning 72 gold medals in a count by the Bangkok Post.
There were 33 events at the Myanmar Games, including traditional sports such as chinlone, vovinam, kempo and muay (Muay Thai).
Before the Myanmar tournament, Thailand complained there were too many local sports and only targeted second place in the medal standings.
Sakol Wannapong, deputy governor of the Sports Authority of Thailand, yesterday praised all sports associations for the preparations of their athletes.
"Overall, they did better than expectations. Credit to those involved in preparing their athletes for the Games," he said.
"They worked hard and deserved their great results. It is a great present for all Thais when the country is hit by political problems."
Thailand won in many popular events, including men's and women's football and volleyball, he said.
The most disappointing Thai team was the shooting squad, which won only two golds, according to Sakol.
"This was a result of conflict within the association," he said.
Sakol said the fine performance will be a major boost for Thailand's campaign at the 2014 Asian Games in Incheon, South Korea.
Among Thailand's 32 sport associations which took part in the Myanmar Games, 11 associations did better than their pre-tournament target, including weightlifting, swimming and athletics.
At the same time, 11 associations met their goal and 10 failed to live up to expectations.
Thana Chaiprasit, Thailand's chief of delegation, said many countries congratulated Thailand for winning the overall championship during yesterday's meeting.
Thana also praised the hosts for doing a good job in staging their first SEA Games for 44 years.
"I give them eight out of 10 points. They did it quite well," said Thana, who has been involved in the SEA Games for nearly two decades.
He said he did not give Myanmar a higher mark because of poor officiating in certain events.
"If they are to host a bigger tournament, they need more qualified match officials," he said.
Pisanu Suvanajata, the Thai ambassador to Myanmar, was satisfied with the performances by his compatriots. He also praised Myanmar for running a great tournament.
"Before the Games started, a large number of people were unsure how well the Games would be run because they had not staged the event for a long time," he said.
"But they were determined to show the world a great tournament. They prove they can do it. With their sporting facilities and marvellous local fans, I think they can stage a bigger event, such as the Asian Games, in the future."
Thailand's success at the Myanmar tournament was costly, though, as the National Sports Development Fund will have to pay the successful athletes, coaches and associations a huge sum in bonuses.
According to the organisation's bonus scheme for the SEA Games, a gold medallist gets 200,000 baht, a runner-up 100,000 baht and a bronze winner 50,000 baht. Separately, their associations receive 30 percent of the total sum their athletes get and the coaches 20 percent.
Based on the medals Thailand won, the agency will have to pay them about 166 million baht (110 million baht for the athletes). The Rowing and Canoeing Association of Thailand and their athletes will get the biggest share of about 52 million baht.
The next Games will be held in Singapore in 2015.