Sakalauskas, who currently heads the Klaipeda State Musical Theater and is a member of the El Fuego vocal group, was chosen from 13 applicants.
He will be screened by security services before being appointed for a five-year term as LNOBT head, the ministry said.
Sakalauskas in 2010 received his Master's Degree in Opera Singing from Lithuanian Academy of Music and Theater (LMTA).
The first attempt to find a new director general failed last October as none of the eight applicants met the minimum requirements.
Sigitas Žutautas, a financial manager, has been serving as acting head of LNOBT since last June, when Gintautas Kėvišas was fired from the job of director general, which he had held for 15 years, for placing himself in conflict of interest situations.