Indonesia eventually won the game 5-2 at the Olympic Stadium in Phnom Penh, but the victory was overshadowed by scenes of violence that saw only eight Thai players left on the pitch at the final whistle.
Thai tempers flared on the stroke of halftime when Indonesia went 2-0 up. Muhammad Ramadhan scored his second goal of the game after stealing the ball as it was being passed back by Indonesia after a stoppage.
The sense of injustice seemed to fire up Thailand, who took control of the game in the second half. Forward Anan Yodsangwal duly reduced the deficit in the 65th minute, heading in from a corner, but Thailand struggled to find an equaliser to force extra-time.
Time seemed to have run out when Indonesia began celebrating as the referee blew the whistle after 90 minutes. But he had signalled a Thai freekick rather than full-time.
From the free-kick, Yotsakorn Burapha collected the ball in the area, evaded an Indonesian defender and smashed home to draw Thailand level in the 98th minute.
Several Thai players and staff then ran over to the Indonesian bench to rub in the pain, which led to a confrontation and shoving.
Simmering anger exploded into violence on the sidelines when Ifan Jauhari scored straight after the restart to make it 3-2 for Indonesia. Uniformed security guards struggled to halt the fighting as both benches exchanged blows in a mass brawl. Thai goalkeeper Soponwit Rakyart swung a left hook at an Indonesian player in the melee and was shown a red card. Indonesia’s Komang Trisnanda and a Thai member of staff were also dismissed.
The FAT apologised for the incident on Wednesday, saying had damaged the Thailand national team's image. The association said it will submit an official apology letter to the organisations affected. It said players and staff representing Thailand have a duty to keep their cool in tense situations, and vowed tough punishment over Tuesday night’s violence.
"There will be severe punishment for those found to have caused the incident," said the FAT statement. It said a committee will be set up to conduct an investigation once the Thailand team returns home.
"The association is ready to accept all suggestions to improve performance and prevent a repeat of this incident," it added.