Israel halted fuel supplies and shut all border crossings with Gaza on Friday in response to ongoing insurgent rocket attacks from the territory, controlled by Islamist group Hamas.
Ministry spokesman Arye Meckel said the decision to relax the blockade had been approved by Defense Minister Ehud Barak and would be a one-off measure.
"We will monitor the situation and then decide on further actions," the spokesman said, adding that medicine will be allowed through the border along with the fuel.
The fuel is needed for Gaza's only power plant to resume operations after power was cut off to most of the Palestinian enclave, home to 1.5 million, triggering the closure of factories and filling stations.
Hospitals switched to backup electricity supplies, but health officials warned that patients could soon be at risk if the situation did not change. The United Nations has condemned the blockade.