Broadcasts from the radio station had brought airport traffic at Ben Gurion to a standstill several times because of interference to control tower communications.
Airport staff had threatened to go on strike if the broadcasts were not stopped.
Airport authorities have said the problem occurs regularly but that traffic controllers can usually find alternate frequencies and rarely cancel flights.
But late on Wednesday, all takeoffs at the airport were canceled after the pirate broadcasts disrupted all the frequencies used by air traffic controllers, Uri Orlev, an airport official, told Army Radio.
The pirate broadcasts were a "clear danger" that "do not allow us to run the airport as we should," Orlev told Israel's Channel 2 TV and appealed to the government to put pirate radio stations out of business.
Haaretz reported on Thursday that Israel's Communications Ministry planned to tackle illegal radio stations by fining advertisers who use their broadcasts and thereby cut revenues to the stations.