A small group of Israelis was approved by a government committee to land in Ben-Gurion Airport on Saturday night, Ynet reported.
The United Airlines flight, UA91, was permitted to take off from New York.
This is the second instance where a flight with Israelis was approved to land at the airport, contradicting the government-mandated closure for passenger flights, which was enacted last week.
Earlier on Saturday evening, Israeli airline company Israir announced that two flights carrying stranded Israelis will take off toward Ben-Gurion Airport on Monday.
These rescue flights are meant for Israelis who flew abroad and found themselves stuck overseas when the airport shut down.
It was reported on Wednesday that several cancer patients were scheduled to fly to Austria for treatments, but were denied access due to the airport closure.
Prime Minister Benjamin Netanyahu and other senior ministers had decided as part of the shutdown measures that anyone wishing to cross Israel's borders would require special permission.
The country was sealed off to prevent variants of the coronavirus from infiltrating state borders. Three known mutations of the virus have not yet been discovered in Israel.
"It would be advisable for us to shut down, or at least limit as much as possible the air traffic," Cyrille Cohen, head of the immunotherapy laboratory at Bar-Ilan University told The Jerusalem Post last week. "We are counting on vaccines."