The raid came after a rocket fired from the Hamas-controlled Gaza Strip hit the Israeli city of Ashkelon.
The attacks are the latest violations of ceasefires declared by both sides after an Israeli assault on Gaza meant to stop militant rocket fire on Israel.
Meanwhile, US Secretary of State Hillary Clinton promised a sustained effort to create a Palestinian state.
Speaking to reporters with Middle East envoy George Mitchell, newly-returned from his first visit to the region, she promised to work towards a "negotiated agreement that would end the conflict between Israel and the Palestinians".
Hamas and Israel declared separate ceasefires on 18 January after Israel's three-week attack on the Gaza Strip.
About 1,300 Palestinians and 13 Israelis died in fighting as Israel tried to halt or significantly reduce militant rocket fire, and to degrade the military capability of Hamas.
Israel had warned of a harsh response to any further rocket fire from Gaza after the long-range Grad rocket hit Ashkelon on Tuesday.
It was the first attack on Israel involving a Grad rocket since the ceasefires.
Other rockets and mortars have been launched from Gaza, however, and Israel has bombed targets in the narrow coastal territory.
No casualties have been reported in either of the latest attacks.
"I suggest Hamas doesn't fool around with us," said Israeli Defence Minister Ehud Barak.
"The air force is operating in Gaza as we speak. We promised calm in the south and we will keep our promise."
Residents of Rafah, on the border with Egypt, said they received telephone calls from the Israeli military warning them to leave their homes ahead of the air raid.
The town is the location of many of the tunnels used to smuggle goods, including weapons, into the Gaza Strip.
There has been no word on which group was behind Tuesday's rocket attack, but the Israeli prime minister's spokesman, Mark Regev, accused Hamas of trying to undermine the ceasefire.
Ashkelon, a city of 122,000 people, is 12 km (7 miles) from northern Gaza.
The city is out of range of the standard rockets and mortars fired by Palestinian militants. Factory-produced Grad rockets, which are smuggled into Gaza from neighbouring Egypt, have a longer reach.
Both Hillary Clinton and George Mitchell promised a long-term effort to negotiate an end to the Israeli-Palestinian conflict.
"This is the first of what will be an ongoing, high level of engagement," Mrs Clinton said of Mr Mitchell's trip.
"We want to send a clear message... that the United States is committed to this path and we are going to work as hard as we can over what period of time is required to try to help the parties make progress together."