The United Nations had said last week that stocks of wheat, sugar and cooking oil were dwindling in Gaza and could begin to run out within days unless Israel reopened the Karni crossing.
"The decision to open the crossing was made despite existing security alerts and after both humanitarian and security aspects were taken into consideration," the Israeli army said in a statement on Thursday.
Salim Abu Safiyah, director of security at Palestinian crossings with Israel, said Karni was reopened partially for food and medicine. Trucks were not allowed to leave Gaza for Israel yet, but might be able to from Sunday, he said.
"It is a step in the right direction; but it is not enough. We need the crossing to open as normal and to be in full operation," he told Reuters.
Israel closed Karni for 21 days between 15 January and 5 February. It was closed again on 21 February after an explosion in the area and had remained shut because of "continued security alerts", the army had said.
Israeli officials had defended the closure as a security precaution against possible Palestinian attacks and said they offered to reroute supplies to Gaza through another crossing, a proposal the Palestinians had declined.
The Palestinians say such closures are collective punishment.
Over 500 tonnes of produce grown in Gaza greenhouses had to be destroyed in the last week because of the Karni closure, a US government report has said.
Israel ended its 38-year military rule of the Gaza Strip last year, but retains control of all access points for bringing goods in and out of the territory.