It was the first time that Israel has deployed its "Iron Dome" rocket defence system in Eilat, a normally placid resort near Egypt's Sinai peninsula that is popular with Israeli and European tourists.
The incident came after days of heightened tension along the Egypt-Israel border fueled by an Egyptian crackdown on militant groups. The area has experienced increased militant activity since the ouster of long-time Egyptian President Hosni Mubarak two years ago.
Yaalon said it was "no coincidence" that Iron Dome had been deployed near Eilat.
"In general in Sinai now, as we have seen for a long time, there is radical Islamic terror there that mainly attacks the Egyptian military and police but is also trying to attack us," he told reporters during a stop in northern Israel.
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Last Thursday, Israel briefly closed Eilat's airport in response to unspecified security warnings. The following day, five men believed to be Islamic militants were killed in the Sinai, and a rocket launcher there was reportedly destroyed, according to Egyptian officials. Egyptian security officials attributed Friday's strike to a drone fired from the Israeli side of the border, but Israel has remained silent about the attack.
Another group, Ansar Jerusalem, earlier sent an email claiming it had fired the rocket. But the group's statement did not appear on the militant websites, which are often used by al-Qaeda and other extremists to publish information.
Israel and Egypt signed a peace treaty in 1979, and while relations have never been warm, the agreement has been a cornerstone of regional security for the past three decades.