A clever finish by forward Sarawut Masuk on 21 minutes was enough to hold off the hard-working Indonesians -- who were runners-up and silver medalists for the second tournament in a row.
Singapore earlier took bronze after beating defending champions Malaysia 2-1.
The Thais went into the final as hot favourites after trouncing the Indonesians 4-1 in the group stage and going unbeaten for the whole tournament.
But there was to be no repeat of that cake walk in an absorbing, tight encounter.
The Indonesian midfield recovered from a cagey start to take control of the game, but the side lacked conviction in the final third allowing the Thai defence to easily mop up attacks.
For all their endeavour it was the Thais who struck first.
The deadlock was broken on 21 minutes as Thailand's Sarawut Masuk cut through the Indonesian backline with a one-two before chipping the ball exquisitely over the advancing goalkeeper.
Thereafter Thailand appeared content to absorb pressure and launch the occasional counter-attack.
While Indonesia huffed and puffed they carved few clear chances, although the industrious Ramdani Lestaluhu clipped the outside of the post on 75 minutes after a melee in the goal area.
At the final whistle the delighted Thai bench streamed onto the pitch to celebrate with their teammates, while the inconsolable Indonesians sunk to the turf at Naypyidaw's purpose-built Zayar Thiri Stadium.
It was the second narrow SEA Games loss for the Indonesians, who fell on penalties at home to Malaysia in the 2011 final.
The result gives the Thais gold for the first time since 2007.
It also secured a double gold for Thai football after the women's team overcame Vietnam in the final on Friday.
Fiercely contested but little known outside the region, the SEA Games are held every two years, giving athletes from lesser sporting nations a chance of medal glory.
Myanmar's hosting of the Games has been seen as a 'coming out' party for the former junta-ruled nation as it undergoes sweeping reforms.
Thailand leads the medals table with 106 golds with one day of competition to go while the hosts are in second on 84 golds.
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Thailand's Praweenwat Boon Yong celebrates after scoring a penalty for a 1-0 lead against Singapore in the football semifinal during the 27th SEA Games in Naypyidaw's Zeyar Thiri Stadium, Myanmar, on Dec 19, 2013. -- Photo: Kevin Lim
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