The report said Israeli jets entered Syrian airspace close to 6 a.m Saturday and flew over Assad's palace in Damascus and other security facilities before striking a chemical weapons compound near the city.
The Hebrew language daily said a Syrian army air defense battery positioned in the city fired at the Israeli jets, but the aircraft left Syrian airspace unscathed. FSA rebels posted a video showing smoke rising from the headquarters for chemical weapons.
There were no reports of the extent of damage or casualties.
Neither Damascus nor Jerusalem responded to the report.
In January, foreign media reported Israeli jets bombed a weapons convoy parked outside a military research institute near Damascus allegedly en route to Hezbollah in southern Lebanon.
The Syrian Network for Human Rights said it documented 88 deaths due to violence across Syria Sunday, including 12 children, eight women, five torture victims and 35 armed rebels.
The organization said 23 of the deaths occurred in Aleppo, 16 in and around Damascus, 13 in Idlib, 12 in Hama, 10 in Homs and nine in Daraa.