The 1-0 scoreline in Bangkok tonight meant Singapore beat Thailand 3-2 on aggregate in the two final games.
Singapore had beaten Thailand 3-1 in the first leg of the final, held at the Jalan Besar stadium in Singapore on Wednesday.
But Singapore clung on to their advantage in the return leg at Bangkok's Supachalasai stadium, despite near-relentless pressure from the spirited Thais.
Thailand's War Elephants threw everything at the visitors and dominated the game, with a bullet header from Kirati Keawsombut just before half-time giving them hope of securing a famous victory in front of fevered home support.
But they could not find a second goal to take the game into extra-time, with Singapore's defence resolute in the face of wave after wave of Thai attacks.
The Thais needed to score at least two goals to force extra time and stand any chance of ending a 10-year Asean title drought.
Both countries were vying to become the first four-time winners of the Southeast Asian championship, which was launched in 1996.
The War Elephants last won the biennial event in 2002, while Singapore's third title came in 2007 when they beat Thailand in the final.
"We surely can come back," Thailand coach Winfried Schaefer said before the match.
Schaefer conceded, though, that his team needed to attack from the start and stay focused throughout.
Earlier, Thailand captain Panupong Wongsa said he and his teammates would leave no stone unturned in pursuit of victory.
For Singapore coach Radojko Avramovic the victory was especially sweet, as he said earlier that he would be leaving his position after the match.
The 63-year-old Serbian took over as Singapore coach in 2003 and led the Lions to two consecutive AFF titles in 2004 and 2007.
He also led Singapore to the third round of the Asian qualifying for the 2010 World Cup, a first for the Lions.