Deputies said members of the General National Congress (GNC) would choose between Misrata businessman Ahmed Miitig and Benghazi academic Omar al-Hassi.
They won Tuesday's first round from an initial field of seven candidates, with 67 and 34 votes respectively out of the 152 deputies present.
A second round of voting due to have taken place on Tuesday had to be postponed when gunmen stormed into the assembly.
It was not known who the gunmen were or why they burst into the building.
Today, 152 deputies gathered amid no visible increase in security to vote for the new premier, the third in just a few months in the North African nation still rocked by violence 30 months after the rebels killed Kadhafi in October 2011.
Some lawmakers, convinced that neither Miitig nor Hassi would secure the 120 votes necessary to win the second round, had proposed that the new prime minister be elected by a simple majority vote instead.
But he would then be subject to a vote of confidence in which he would need to secure 120 "for" votes.
The vote for a new prime minister comes with the GNC in the grip of a power struggle between Islamists and liberals.
The election was triggered by the resignation of interim premier Abdullah al-Thani earlier this month, who quit just five days after his appointment, saying he and his family had come under attack.
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