A Palestinian health ministry spokesman in the Gaza Strip said there were no casualties in the air strike, which came just hours after the rocket hit an open field in southern Israel on Friday without causing casualties or damage.
It was the third time a rocket fired from the Palestinian enclave struck within Israel since the August 26 truce between Israel and Palestinian Islamist movement Hamas, the territory's de facto rulers.
The Israeli army said the air strike in the southern Gaza Strip had "targeted a Hamas terror infrastructure site".
Defence Minister Moshe Yaalon said the target was a concrete factory being used to repair tunnels in and out of Gaza, dozens of which Israel destroyed during the summer campaign.
The attack was "an unequivocal message to Hamas that we will not tolerate a return to a routine of sporadic firing at our citizens," Yaalon said, vowing Israel would "act forcefully" against Hamas "if it won't prevent attacks".
And Prime Minister Benjamin Netanyahu reiterated that Israel would not ignore "even one rocket launch" at its territory.
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"Hamas will bear the consequences of any escalation that might take place," he told soldiers at a ceremony in remarks distributed by his office.
Hamas did not say it was behind the rocket attack, but Israel holds it accountable for any rocket fire from Gaza.
Gaza's Hamas leader Ismail Haniya condemned Israel's "dangerous violation of the ceasefire", and in remarks to reporters urged Egypt to "move with urgency" to ensure the Jewish state respects the agreement.
The summer war between Israel and Hamas killed almost 2,200 Palestinians, most of them civilians, and 73 people on the Israeli side, nearly all of them soldiers.
The Egypt-brokered ceasefire was to have been followed by talks on a more lasting truce, but they were called off amid deteriorating ties between Cairo and Hamas.
Also on Saturday, the navy fired warning shots after fishing boats sailed beyond the six nautical mile limit enforced by Israel off Gaza's coast.
A military spokeswoman told AFP the vessels returned to waters where the navy allows them to operate.