Militants fired two rockets towards Israel's main metropolitan area, both of which landed in open ground, the IDF said.
There have been no reports of fatalities, and it remains unclear who carried out the launches.
The Israeli military said its Iron Dome aerial defense system did not make any interceptions of the rockets, despite early reports to the contrary. It stressed that its alert and warning system had operated as required.
About four hours after the launches, the IDF announced it had begun striking targets in Gaza in response. Reports from inside the territory said sites around Khan Younis in the south of the Strip were among the first to be hit.
Militant factions in Gaza have denied carrying out the launches.
The Qassam Brigades, the armed wing of the Hamas militant group that runs Gaza, has said it was not responsible.
In a statement sent to journalists, a Qassam Brigades spokesman drew attention to the fact that the launches had taken place during a visit to Gaza by a security delegation from Egypt, which has been leading mediation efforts between Israel and Hamas.
And a spokesman for Islamic Jihad, a smaller militant group in Gaza, also told CNN it denied suggestions that it had carried out the rocket launches.
The launches come at a delicate moment.
Not only is Egypt in the midst of another effort to achieve a long-term ceasefire between Israel and Hamas, but Israel is just weeks away from a general election.
Prime Minister Benjamin Netanyahu, who also serves as the country's defense minister, met with his military chiefs to decide on Israel's response.
A short while after Israel began its retaliation, sirens sounded in an area immediately to the east of Gaza indicating a further rocket launch.
The IDF said it believed a rocket had been fired from Gaza but that it had failed to make it into Israeli territory,
Andrew Carey reported from Jerusalem and Ibrahim Dahman from Gaza.