"The terminal reopened at 8am (0600 GMT) and will stay open until 5pm (1500 GMT)," said a Palestinian security source.
The crossing point will be open for all Palestinians travelling in either direction during Saturday.
The vital terminal, whose operation is dictated by the Israelis on security grounds, had been closed almost continuously for three months until Friday when it was opened for two days ahead of Ramadan.
On Friday, access to Egypt from Gaza was granted only for humanitarian cases, for students and for pilgrims heading for Makka in Saudi Arabia, according to European Union observers at the terminal.
There were no restrictions on those wanting to travel from Egypt into Gaza. A total of nearly 4,000 people crossed the border point during Friday.
"Israel has agreed that the terminal opens during the two days but we hope that it will remain open afterwards," added a spokesman for the observers who are deployed at Rafah at the request of the Palestinian Authority and Israel to monitor agreements on border traffic.
Since late June, when fighters from Gaza killed two Israeli soldiers and seized a third in a cross-border raid, the crossing has been open for a total of only about seven days.
Thousands of Palestinians have been stranded on either side for weeks.
There were reports on Friday that unidentified armed men set off a small bomb near Palestinian police guarding European Union monitors at the border shortly after it opened.
Two Palestinian policemen were injured, but none of the EU monitors was hurt, Hatem Barhoum, a senior police official in Gaza, told AP news agency.
Police responded first by firing into the air and then at the suspects, who were armed with automatic weapons, Barhoum said.