Israel rushed forces and tanks across the border into the northern Gaza Strip after the raid. Palestinian officials said four people were killed in tank shelling and an Israeli airstrike on a car carrying militants near Gaza City.
Islamic Jihad and a smaller armed faction, the Popular Resistance Committees, claimed responsibility for the raid at the Nahal Oz terminal, just across the border from Gaza. Israeli government spokesman Mark Regev said Hamas militants, who control Gaza, were "responsible and will be held accountable."
The Popular Resistance Committees has close ties with Hamas.
Fawzi Barhoum, a Hamas spokesman, praised the attack as "heroic and courageous." He said Hamas was not responsible but affirmed his group's support for "resistance."
Islamic Jihad spokesman Abu Ahmad called the raid a "unique and complicated operation." He said details would be released later, but Israeli media said the militants had fired a series of mortar shells before the infiltration to divert Israel's attention.
Channel 2 TV said the militants cut through a border fence to enter Israeli territory, killed two workers at the fuel terminal, and set fuel depots afire.
Two attackers were killed as troops returned fire, but others fled back into Gaza, the Israeli military said.
Residents of nearby border communities hunkered down in their homes, even after the violence subsided.
Islamic Jihad said one gunman was killed when Israeli aircraft struck outside Gaza City shortly after the raid. Tank fire in the area killed three civilians, and wounded 10, Palestinian hospital officials said.
The military said the tank fire killed two militants.
Munther Rahmi, a worker on the Palestinian side of the border, said he saw Israeli tanks crossing into Gaza.
"We are surrounded by tanks. It's a war out there," he said.
The attack upset a period of calm after a broad Israeli military offensive that killed more than 120 Palestinians, including dozens of civilians. Since the offensive ended in early March, Egypt has been trying to mediate a cease-fire between Israel and Hamas.
Although violence had subsided, tensions have been increasing in Gaza, whose 1.4 million residents have been confined to the territory since Hamas wrested control there in June.
On Tuesday, Hamas threatened to burst across the Israeli border to end Israel's blockade of Gaza, imposed after the militant group's takeover.
A Hamas militant and an Israeli soldier were killed in earlier clashes in southern Gaza Wednesday. The military said it launched a brief ground operation and airstrikes there in response to shooting attacks and other anti-Israel activity.
Last week, an aide to Israel's public security minister was wounded by a Palestinian gunman as he and the minister toured an observation point overlooking Gaza with a group of Canadian tourists.