The leader of the progressive National Front Party was picked over rival Ali Zidan by a vote of 113-85, the Libya Herald reported.
Zidan had led Magarief 80-56 after the first round of balloting Wednesday evening. Union for Homeland leader Abdulrahman Sewehli received 53 votes and two other candidates split nine other votes.
Magarief picked up the lion's share of Sewehli's votes in the runoff.
The newspaper said Magarief, as speaker, is effectively Libya's acting head of state, though the extent of his power remains to be seen.