The designation was approved by 58 votes in a secret ballot during the parliament's plenary, while 25 were against and four abstained.
The bid to appoint Antanaitis was strongly criticized by some of the opposition and eight members of the new line-up of the 17-member commission, questioning his competences.
MP Eugenijus Jovaiša of the ruling Lithuanian Farmers and Greens Union, the chief of the parliamentary Education and Science Committee who picked the candidate, accused the opposition of political games.
Antanaitis has come under criticism for his work in alkas.lt news portal, which published a list of parliamentarians proposing a bill on the original spelling of last names and dismissed them as traitors of language.
Antanaitis said he had nothing to do with the list.
Proposed to the commission by the Lithuanian Union of Journalists, Antanaitis is currently the publisher and editor of alkas.lt that claims to propagate the Baltic world outlook.