Hisham Edwan, head of the operations at the crossing, told Xinhua news agency that the first bus had already left the Palestinian side and those stranded on the crossing can cross back to Gaza.
The Borders Control Commission run by the Islamic Hamas movement in Gaza said the crossing would be open only on Saturday and Sunday and only for those already registered at the Hamas Interior Ministry as well as humanitarian cases.
Hundreds of Palestinians gathered in Khan Younis, south of Gaza Strip, to take bus to the crossing.
Deputy Interior Minister Kamel Abu Madi said opening the crossing for only two days was not enough for the registered and humanitarian cases.
Last Tuesday, Egypt opened the borders exceptionally for three days to allow 2,329 Muslim pilgrims to leave Gaza to Saudi Arabia, but did not allow Palestinians to cross back into Gaza.
The last time the crossing was opened in both the directions was on June 29 for five days. That was one of the four times the borders opened this year.
Gaza's Interior Ministry data said there were over 25,000 humanitarian cases registered for travelling through the border crossing.
The coastal territory, home to some 1.9 million people, has been blockaded by Israel since Islamic Hamas movement seized control of the tiny enclave by force in 2007 after routing troops loyal to Palestinian president Mahmoud Abbas, who now rules the West Bank.
Egypt, which also shares border with Gaza, has been imposing restrictions on opening the Rafah crossing with the enclave after the removal of Islamist President Mohammed Morsi in 2013.
