Playing in the first leg of the final at Pakansari Stadium, Thailand's Teerasil Dangda managed to secure the first goal of the match in minute 33.
Thailand soon led the game with players who seemed to dominate,but Indonesia didn't give up their hopes of winning the title for the first time.
Cheered on by around 30,000 supporters, the home team fought hard to win the match.
Indonesia's Rizky Pora secured a goal in minute 66, earning a huge cheer from the crowd.
Less than five minutes later, Hansamu Yama struck another goal for Indonesia, the home side now leading the game 2-1.
The match was the fifth time Indonesia has made it to the final in the championship, but it has never yet won the title.
Indonesia's success in the first leg comes as a surprise, as it entered the tournament without having played any competitive matches since the last AFF Suzuki Cup in 2014.
The country had previously suffered under a one-year ban from international events imposed by world soccer body FIFA.
The AFF Suzuki Cup is the first international tournament for Indonesia after the ban was lifted in May.
The second leg of the final will be played on Saturday in Thailand, which has won the AFF Suzuki Cup four times.
