Assad was staying at his holiday home in the northern Syrian city of Latakia when the planes flew overhead last Sunday, Israel-based Channel One television said on Friday.
Israeli warplanes have not overflown Syria since Israel ended a 22-year occupation of South Lebanon in 2000. Syria has long been the dominating outside power in Lebanon and has had forces there since its civil war began in the 1970s.
Syria made no comment on the Israeli report.
Israeli planes also broke the sound barrier over the Lebanese capital, Beirut, earlier this week, shaking buildings and setting off car alarms in retaliation for Hizb Allah shelling that killed an Israeli teenager on Sunday.
Lebanon and Hizb Allah say repeated Israeli intrusions into Lebanese skies are to blame for the flare-up on Israel's northern border.
The Israeli fatality from Hizb Allah shelling was the first since the Jewish state withdrew its forces from southern Lebanon in May 2000 after a 22-year occupation after daily guerrilla attacks by Hizb Allah resistance forces.