Palestinian militants blew through the wall between Gaza and Egypt on Friday, allowing hundreds of Palestinians to return to their homes in Gaza.
Palestinians have been stuck behind the border for weeks
They had been stranded on the Egyptian side since the border was closed more than two weeks ago, after two Israeli soldiers were killed in an attack.
Israel attacked the Palestinian economy ministry in Gaza City early on Saturday as its military operations continued.
Earlier Israeli troops withdrew from central Gaza after a two-day incursion.
The Israeli forces moved back over the border on Thursday night after holding a swathe of territory around the town of Khan Younis.
Sixteen Palestinians, mainly militants, died during the operation.
The incursion was part of a two-pronged effort which Israel says is aimed at rescuing captured Israeli soldier Cpl Gilad Shalit, and reducing the number of rocket attacks by militants against Israeli towns.
Israeli forces remain in other parts of the Gaza Strip.
On Friday about 70 gunmen assailed the border between Gaza and Egypt at Rafah, blowing a six-metre (20-foot) hole in a frontier wall.
Hundreds of people then forced their way past Palestinian and Egyptian border guards.
Some walked through the breach carrying suitcases, others ran, while others hobbled through on crutches.
Some cheered "God is greatest".
Rafah is the only land border between Gaza and the outside world, apart from those with Israel.
Israel is worried that militants who are holding Cpl Shilat in Gaza might try to smuggle him out of the territory, says the BBC's Alan Johnston in Gaza.
Thousands of Gaza residents have been stranded on the Egyptian side since the border was closed, Palestinian security sources say.
Israel says its operations will continue in other parts of Gaza
Several people have been reported to have died from heat exhaustion in that time.
Eventually, Palestinian government forces did manage to secure the area around the border and stop movement through the hole in the wall.
Elsewhere, Israeli warplanes fired on a bridge and a Hamas office in Gaza, while witnesses said Israeli bulldozers destroyed a large part of the main central road.
On Thursday, the United States vetoed a UN resolution calling on Israel to halt its military operations in Gaza.
Washington's UN ambassador, John Bolton, said the resolution laid disproportionate blame on Israel for the current crisis.
Ten Security Council members voted in favour of Qatar's motion, while four abstained.
Israel has rejected calls for a ceasefire, and says it will not enter into negotiations for Cpl Shalit's release.