Prayuth received 264 votes in favour and 208 against on Saturday. Health Minister Anutin Charnvirakul and four other cabinet ministers also survived the censure motion in a similar fashion.
The opposition needed 242 of the 482 parliamentary votes to remove the prime minister.
Prayuth said he remained confident after the vote.
Lawmakers over four days accused his government of mishandling the pandemic and criticised him for the severe economic impact, taking aim at the government’s slow vaccine rollout as a result of not making advance vaccine orders and deciding not to join the international COVAX vaccine-supply scheme.
Prayuth has stood by those decisions.
This is the third censure motion the government has survived and comes as pro-democracy protesters plan more demonstrations on Saturday.
Recent rallies have turned violent, with security forces using tear gas, water cannon and rubber bullets against protesters who threw stones and firecrackers.
Thailand has reported more than 1.2 million infections and nearly 12,000 coronavirus-related deaths, most of them since April due to the Delta variant.
Authorities reported the largest single-day increase in cases in mid-August with more than 23,000 cases.
The vaccine rollout began in June amid the country’s severest outbreak, with people unable to find medical treatment and some dying at home. About 13 percent of Thailand’s more than 66 million people have been fully vaccinated.