At Olympic Stadium in Phnom Penh, an Indonesian Ramadhan Sananta netted two goals in the first half of normal time before Thailand’s Anan Yodsangwal made it 2-1 in the 64th.
Yotsakorn Burapha's last-second goal made it 2-2 before extra time was added, giving Thailand some hope.
Tensions boiled over between the two nations during the additional time, resulting in three Thai players receiving red cards and three more goals being conceded.
The 5-2 victory over the War Elephant made Indonesia the competition's three-time champion.
Thailand, which has won the title the most at 16, has been the second place for two consecutive times.
Thai national team players will return to Thailand on May 17.