Transport Minister Marius Skuodis said at the Cabinet's meeting that the airspace would be closed to Russian air carriers from midnight, with "certain exceptions".
"These are related to emergency landings, humanitarian flights," he said.
Latvia and Estonia also announced their decisions to ban Russian aircraft from their airspace on Saturday.
According to Lithuanian Prime Minister Ingrida Simonyte, the Latvian government should also approve the decision shortly, while in Estonia, a ministerial decision is sufficient.
"We have had some coordination so that these are not separate initiatives," she said.
Foreign Minister Gabrielius Landsbergis said that initiatives in response to Russia's war in Ukraine are only effective "when implemented within a group of countries".
"I made it very clear in Brussels yesterday that, please, let's do all initiatives together," the minister said. "Decision-making procedures are different, some require the approval of the government, some require a ministerial decision, and the amount of time it takes differs, so it is better to coordinate."
"We have to keep in mind the legal issues. There are international treaties, bilateral treaties, their evaluation," he added.