A spokeswoman for the Israeli defence ministry unit that oversees the passage confirmed that the Erez crossing had been closed.
Border protests and clashes on Friday left two Palestinians dead by Israeli gunfire.
Israel’s army said firebombs and IEDs were also hurled at the border fence, while a number of Palestinians briefly crossed into Israeli territory.
The closure and border incidents occurred despite attempts by Egypt and UN officials to reach a long-term truce between Israel and Hamas, the Islamist movement that runs the blockaded Gaza Strip.
The spokeswoman for the defence ministry unit, known as COGAT, did not say how long the crossing would be closed.
The Palestinian Authority civilian affairs office in Gaza also confirmed the closure except for medical cases and Palestinians seeking to cross back into the enclave.
Israel has enforced an air, land and sea blockade on the Gaza Strip for more than a decade, but grants permission to a limited number of people to cross for various reasons.
Israel had just last week reopened its only goods crossing with Gaza after closing it to most deliveries for more than a month over border tensions.
Protests and clashes began on the Gaza border on March 30 and have continued at varying levels since then.
At least 171 Gazans have been killed by Israeli fire during that time. One Israeli soldier was shot dead by a Palestinian sniper in July.
There have also been several severe military flare-ups, including three since July.
UN officials and Egypt have been seeking to secure a long-term truce between Hamas and Israel to allow for humanitarian issues in the impoverished enclave of two million people to be addressed.
Israel is demanding calm and a return of the remains of two soldiers Hamas is believed to be holding.
Israel and Hamas have fought three wars since 2008.