The cross-border exchange followed a weekend escalation in violence seen as among the most serious since Israel and the coastal enclaves Hamas rulers fought a war in 2014.
The Islamist militant group was quick to say that it did not seek further confrontation.
Israeli fighter jets "targeted underground infrastructure in the southern Gaza Strip, in response to the projectile that was launched at Israel earlier," an army statement said.
It did not give further details, but Palestinian security sources said several missiles were fired at farmland east of Rafah in the south of the Gaza Strip.
Monday's strikes followed fierce exchanges over the weekend after an improvised bomb apparently planted by Palestinian militants exploded Saturday, injuring four Israeli soldiers inspecting the border fence.
Israel responded by pounding 18 Hamas facilities in two waves of air strikes on Saturday and Sunday, according to the Israeli military.
Israeli ground forces also killed two Palestinian teenagers in the enclave in cross-border fire.
But senior Hamas official Mahmoud Zahar said Monday that his organisation had no wish to see fighting with Israel intensify.
"The resistance does not want to waste its energy on this escalation," he told the Hamas-affiliated Al-Risala website.
Another source close to Hamas said it was sending messages to Israel through neighbouring Egypt, which frequently mediates between the two sides.
The source told AFP that Hamas representatives in Cairo "have officially informed the head of Egyptian intelligence that the movement is not interested in any escalation in Gaza."
"The Egyptian authorities must press the (Israeli) occupation government to stop the aggression and ongoing strikes in Gaza," he added.
The European Union said the flareup was of "real concern", describing the deaths of the Palestinian teenagers as "deplorable" and demanding a halt to rocket fire.
"It is extremely important that the situation does not escalate further and it is crucial that all parties act with restraint," it added.
Palestinians said two people were wounded in the weekend air strikes.
Two of the soldiers were severely wounded in the border blast but their lives were not in danger, the army said.
The Popular Resistance Committees, a loose alliance of militants from various Gaza nationalist and Islamist Palestinian groups, claimed responsibility for the explosion and called it a "heroic act".
Israeli army spokesman Lieutenant Colonel Jonathan Conricus on Saturday described the committees as a "rogue group" but said that Israel nevertheless held Hamas responsible for attacks from territory under its control.
Israeli Defence Minister Avigdor Lieberman pledged to eradicate those behind the Saturday explosion.
"Until we eliminate them, the score remains unsettled," he told Israeli news site Ynet yesterday.
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