Palestinian security forces on Friday opened the crossing for two days to allow the passage of people seeking medical treatment, or studying or residing permanently abroad.
Palestinians took control of Gaza last week after an Israeli dismantling and withdrawal of illegal colonies and military barracks.
Israel shut down Gaza's official gateway to Egypt two weeks ago just before completing its pullout from the coastal strip.
Israel wants it to remain sealed for months, for a technological upgrade and to test the Palestinians' ability to take control in Gaza.
Thousands of Palestinians busted through the border last week after the last of the Israeli troops, but the frontier was later sealed to stop the chaos.
A sealed-off Rafah has reinforced Palestinians' perceptions that they are still occupied by Israel.