The Supreme Court's order, which followed a petition from 17 aid groups, effectively halted an earlier Israeli government decision that barred aid groups for refusing to comply with Israel's new rules.
Israel had announced it would ban 37 aid groups by March 1 for not abiding by rules introduced last year that require aid groups to register names and contact information of employees, and provide details about their funding and operations.
The groups view the rules as invasive and arbitrary, and say the ban would hinder critical assistance.
Israel says the new measures are necessary to ensure armed groups do not infiltrate humanitarian organisations.
A US-negotiated ceasefire reached in October has halted major military operations.
But the two-year war triggered by Hamas' October 7, 2023, attack on Israel has left much of the territory in ruins and most of Gaza's two million Palestinians reliant on international aid.
Israel has also continued to strike what it says are militants, often killing civilians.
Friday's order was a temporary injunction while the court considers the case. There was no timeline for a final decision.
"This is, however, a step in the right direction — with a long, long way still to go" said Athena Rayburn, the executive director of AIDA, an umbrella organisation representing over 100 groups operating in the Palestinian territories.
The Norwegian Refugee Council, among the aid groups facing a ban, welcomed the injunction but said it offers only partial relief.
"The injunction pauses immediate closure," council spokesperson Shaina Low said in a statement.
"It does not restore visas, reopen access or resolve the wider restrictions that continue to affect aid delivery. "
Meanwhile, Israeli airstrikes overnight killed at least five people, four of them members of the Hamas-run police, officials said Friday.
Such strikes have repeatedly disrupted the truce since it took effect in October.
The escalating Palestinian death toll has left many in Gaza feeling as though the war never ended.
Three of the five were killed by a strike on a police checkpoint in southern Gaza near Khan Younis, said Dr Ahmed al-Farra at Nasser Hospital.
Another died in a strike on a checkpoint in Bureij refugee camp, according to a statement from the Hamas-run Interior Ministry, which oversees police in Gaza.
A separate strike in western Khan Younis killed one Palestinian, al-Farra said.
The Israeli military said it killed several militants in Rafah, on the border with Egypt.
It said the strikes were in response to a violation of the ceasefire.
