Service resumed about two hours later. IDF tanks fired at the source, followed by the IAF attack on four positions of Hamas and Islamic Jihad.
The IDF says it does not want an escalation of tensions following a series of strikes on several Hamas targets in the Gaza Strip on Thursday.
They added that the air force also fired four missiles into an area, south of Gaza city, wounding three Palestinians, before they were rushed to the Shifa Medical, center.
The Israeli military twice on Thursday struck targets in Gaza after Israelis working on the border fence came under mortar fire, the Israeli Defense Forces (IDF) said. However, The Israeli military later said the sirens were a false alarm.
The army confirmed shortly thereafter that they had targeted "two additional military posts belonging to terror organizations in the Gaza Strip".
Rival Palestinian factions Fatah and Hamas agreed on Wednesday to delay the final transfer of power over the Gaza Strip from Hamas to the Western-backed Palestinian Authority government by 10 days to December 10 to allow time to "complete arrangements", officials said.
An army spokesperson told reporters that the group fired 10-12 mortar rounds towards an IDF position near a cement factory in a military zone near the border, and that the army knows "by name" who is reponsible.
No group has claimed responsibility for the alleged rocket attack, while Palestinian officials have yet to issue comment regarding the army's assertions.
Sharp disagreements remained between Palestinian President Mahmoud Abbas's Fatah, based in the occupied West Bank, and Hamas, particularly over the fate of public employees in Gaza and security control of the enclave. Occasional exchanges of fire continue to occur along the border.