With the win, Oman finished second in Group D behind Australia. The Gulf team overtook Saudi Arabia, which may have gone through with a draw or even a loss had Oman not won. Instead, Oman got the win and Saudi Arabia was beaten by Australia 4-2.
Oman dominated the match played in the midday heat.Midfielder Hussain al-Hadhri gave Oman the lead in the 10th minute. Thailand was reduced to 10 men when substitute Winothia Teeratep was sent off in the 85th minute for dangerous play.
Oman took advantage and doubled its lead when midfielder Adbul al-Muqbali scored in the 90th.
It was only Oman's second victory in qualifying.
''I am very proud of the team as we did not have the best start in the third round,'' Oman coach Paul Le Guen said. ''But we came back strongly after our away defeats to Thailand and Australia. It shows the team's character and we deserved to win today.''
The win set off wild celebrations across the Omani capital of Muscat, with crowds cheering and waving the national flag.
''It is a victory dedicated to the fans,'' captain Ali Al Habsi said. ''We played a good match and I am proud of my teammates.''
Lineups: Oman: Ali al-Habsi, Mohammed Abdullah Sheeba, Hussain al-Hadhri (Juma Darwish, 72), Abdulaziz Miqbali, Fauzi Basheer, Saad Suhail, Ahmed Mubarak Kanu, Abdulsalam Amur, Hussain Mudhaffar, Imad al-Hosni (Ismail al-Ajmi, 68), Ahmed Hadeed.
Thailand: Thamsatchanan Kawin, Niweat Siriwong, Nutnum Suchao (Sumanya Purisai, 37), Dangda Teerasil, Anuch Kitpongsri, Jirawat Makkharom, Jetsada Jetsawad, Choeichiu Phicitphong, Suree Sukha, Kaewprom Jakkaphan (Winothai Teeratep, 65, red card, 85), Sutee Suksomkit.