The result will be forwarded to Thailand's king Bhumibol Adulyadej for endorsement.
Prayuth was absent from the voting. He was reportedly outside capital Bangkok for attending activities marking the founding of the 21st Infantry Regiment Queen's Guard.
The new PM will select up to 35 cabinet members and an interim government is expected to start operation in Sept.
In addition to members of the National Council for Peace and Order (NCPO), prominent political figures like Democrat Party leader Abhisit Vejjajiva and Chartthaipattana Party chief adviser Banharn Silpa-archa also voiced support for Prayuth to be selected as the prime minister.