Jordan's state TV said the country had resumed air traffic operations, citing aviation authorities. The opening of its airspace came more than three hours earlier than scheduled.
Iraq's aviation authority said security risks had now been overcome.
Lebanon said its airport will resume its activities after the overnight closure, state TV reported.
Iran launched explosive drones and fired missiles at Israel late on Saturday - its first direct attack on Israeli territory in a retaliatory strike that raises the threat of wider regional conflict.
Jordan, which lies between Iran and Israel, had readied air defences to intercept any drones or missiles that violated its territory, two regional security sources said.
U.S. and British warplanes were involved in shooting down some Israel-bound drones over the Iraq-Syria border area, Israel's Channel 12 reported.
