No casualties or injuries have been reported by the Palestinian Health Ministry.
The Ezzedine al-Qassam Brigades – Hamas armed branch – said they retaliated with surface-to-air missiles.
“Our air defence responded to Zionist warplanes in the skies of the Gaza Strip with surface-to-air missiles at exactly 01.35 local time (1035GMT) Tuesday morning,” it added in a statement.
The attack comes after a rocket fired from the besieged Gaza Strip into southern Israel was intercepted on Monday, in the first such attack in months amid soaring tensions over a flashpoint holy site in occupied East Jerusalem.
There were no immediate reports of casualties or damage and no Palestinian group claimed responsibility for the rocket, which Israel claimed was shot down by its Iron Dome interceptor.
Hamas, the Palestinian group that administers the coastal enclave, had warned that any incidents at the Al-Aqsa Mosque compound would be a “red line” after Israeli forces raided the site in East Jerusalem several times in recent days, arresting hundreds of Palestinians and leaving dozens injured.
Palestinians accuse Israel of encroaching at Al-Aqsa during the Muslim holy month of Ramadan. Israel claims Palestinian protesters seek to disrupt Muslim prayer for political ends and to prevent visits by Jews, who are celebrating Passover.
Prior to the rocket attack, Israeli Prime Minister Naftali Bennett accused Hamas of waging a “wild harassment campaign” against Israel. Egypt and Jordan, which inked peace agreements with Israel decades ago and coordinate with it on security matters, have condemned the actions of Israeli forces at the site.
On Friday, at least 152 Palestinians were wounded by Israeli police inside the mosque compound, the latest outbreak in an upsurge of violence that has raised fears of a slide back to wider conflict.
Crackdowns by Israeli forces on protesters who were demonstrating against attempts to forcibly expel Palestinians from their homes in the East Jerusalem neighbourhood of Sheikh Jarrah last year were a trigger for an escalation in violence between Israel and Hamas fighters in Gaza.