Prayut got 264 votes in favor and 208 against. Health Minister Anutin Charnvirakul and four other cabinet ministers also survived the censure motion in a similar way.
The opposition needed 242 of the 482 parliamentary votes to oust the prime minister.
For four days, lawmakers accused his government of mishandling the pandemic and criticized it for the severe economic impact, which aimed at the slow deployment of government vaccines as a result of not making early vaccination orders and deciding not adhering to the Covax International Vaccine Supply Plan.
Prayut has defended these decisions.
This is the third motion of censure the government has survived and comes as pro-democracy protesters plan more demonstrations on Saturday.
Recent rallies have turned violent, security forces have used tear gas, water cannons and rubber bullets against protesters who threw stones and firecrackers.
Thailand has reported 1.2 million infections and more than 12,000 coronavirus-related deaths, most since April due to the Delta variant.
Authorities reported the largest one-day increase in cases in mid-August, with more than 23,000 cases.
The government cut its economic growth forecast for 2021 for the third time, from 1.5% to 2.5% to 0.7-1.2%. The economy shrank by 6.1% last year.