The Thai team opened the scoring in the 34th minute with a strike by Thitiphan Puangchan. Fellow midfielder Worachit Kanitsribampen secured three points when he fired home in extra time.
The win at Markaziy Stadium in Namangan, Uzbekistan gave the War Elephants six points after two games.
Thailand are now second in Group C behind Uzbekistan on goal difference after the hosts crushed the Maldives 4-0.
In their opening match of the tournament, Thailand trounced the Maldives 3-0, while Sri Lanka lost to Uzbekistan 3-0.
The six group winners plus five best runners-up will qualify for the 2023 Asian Cup finals.
The Thais face Uzbekistan on Tuesday at Markaziy Stadium, 10pm kick-off, Thailand time.