Zeidan presented a coalition cabinet on Tuesday (local time), drawn from liberal and Islamist parties, to the national congress, which had rejected his predecessor's cabinet line-up.
The assembly had met on Tuesday to vote but its session was postponed after protesters, angry with some of the nominations, stormed its headquarters.
A televised vote on Wednesday showed that 105 congress members voted in favour of the line-up. The congress is made up of 200 members but not all were present.
"The government was approved. Now the session is over due to the mess outside," congress member Suleiman Zoubi told Reuters.
As congress met amid tight security, Libyan security forces briefly fired shots in the air to disperse a crowd of about 100 protesters outside the building, a Reuters witness said.
Zeidan needed congress' approval to take office. His transitional government will focus on restoring security in the oil-producing country where many militias have yet to disarm since Gaddafi's overthrow last year.
Congress elected Zeidan prime minister this month after his predecessor, Mustafa Abushagur, lost a confidence vote on his choice of ministers, criticised inside and outside the assembly.
