The matches are at Hampden Park in Glasgow on May 31st, with the "away" fixture due to be played in Hungary on June 4th.
The decision comes against the background of the bloodiest-ever Gaza war.
The conflict started after Hamas' October 7th attack, which sparked an Israeli retaliation that has brought a spiralling civilian death toll and levelled vast swathes of Gaza.
"Due to updated intelligence and following extensive security consultations with all key parties, the Scottish FA regrets to confirm that the forthcoming qualifier between Scotland and Israel at Hampden Park on May 31st will now be played behind closed doors," said a statement from the Scottish Football Association.
It added: "The stadium operations team were alerted to the potential for planned disruptions to the match and as a consequence we have no option but to play the match without supporters in attendance."
