Indonesia`s two goals, from Sani Rizki Fauzi and Osvaldo Ardiles Haay, buried Thailand`s lead in the finals.
This is the second time that Indra Sjafri has taken Indonesia to win the AFF, having won the AFF U-19 championship in 2013.
Thailand`s Saringkan Promsupa scored a goal in the 57th minute through a header.
Indonesia equalized in the 59th minute through Fauzi who made a speculative shoot from outside the penalty area. The ball hit the Thai defender before Fauzi converted into a goal.
Indonesia scored the second goal in the 64th minute through Haay.
Reporting by Gilang Galiartha
Editing by Suharto