It said the aircraft fired "warning shots into an open area from where Qassam rockets were launched" to prevent further attacks.
Wednesday's raid occurred some two hours after Palestinian resistance fighters fired rockets from Gaza into the southern Israeli town of Sderot.
There were no reports of casualties in either incident.
Palestinian witnesses said fighters fired two rockets from Bait Hanun in northern Gaza. Israeli military aircraft were spotted flying overhead immediately afterwards.
An Israeli military source said troops found the remains of the rocket near a college in Sderot, a southern Israeli town targeted in rocket attacks on Monday after Israel killed a leading Islamic Jihad commander.
Palestinian fighters had launched rockets at the same area on Monday in retaliation for Israel's killing of the Islamic Jihad commander in a West Bank raid.
Israel had responded on Monday with air strikes in Gaza, wounding a Palestinian woman and her two daughters, medics said.
The strikes destroyed two buildings linked to Islamic Jihad and fighters from Palestinian President Mahmoud Abbas' ruling Fatah party.
Israel has vowed to retaliate for any Palestinian fire from Gaza since it withdrew from the coastal strip last month, ending 38 years of military occupation.
The flare-up of violence has threatened to unravel an eight-month-old ceasefire.