The European Border Assistance Mission, which monitors the crossing point, said it was unclear when it would reopen.
"It is closed. The operation has stopped for a while until the situation with Haniya is clarified," a spokeswoman said.
Hundreds of Hamas supporters waving the group's green flags had gathered at the Rafah terminal to welcome Haniya's return.
|"This is a political message to the Hamas government and the Palestinian administration as a whole."|
The crossing is the only way in or out of the Gaza Strip that does not involve travelling through Israel.
Nour Odeh, Al Jazeera's Gaza correspondent said: "This is a political message to the Hamas government and the Palestinian administration as a whole."
"This will reinforce the Palestinian conviction that Israel remains an occupying power in the Gaza Strip," she added.
Haniya received assurances of up to $350m in aid for next year during his regional trip, which included visits to Qatar, Iran and Sudan.
Egyptian security sources said that Haniya was carrying $35m.
The Hamas-led government has needed to secure funds this way because of an economic blockade by Western nations and the refusal of the Israeli government to hand over revenue it collects on the Palestinians' behalf.
Haniya had "moved up his return because of the situation in the Palestinian territories", Ahmad Yussef, a senior Hamas official told AFP news agency.
Hamas and Fatah have blamed each other for a series of killings in the Palestinian Territories, the most prominent of which was the shooting of the three young sons of a senior Fatah loyalist on Monday.
That attack was followed by the murder of a prominent Hamas member on his way to work in the southern town of Khan Yunis on Wednesday.