Thousands of Palestinians, many of them carrying empty fuel canisters, managed to push through several openings despite the presence of the Egyptians deployed nine rows deep in some places.
At one point, guards aimed a water cannon above the heads of people, not at them, to keep them back.
Cranes were positioned next to the border, lifting crates of supplies over into Gaza.
Egyptian forces took up positions a few steps into Palestinian territory, using shields to protect themselves from some Gazans who climbed atop car roofs and threw stones at them.
Violence erupted at the Rafah border after Cairo announced it would close the crossing between Gaza and Egypt.
Al Jazeera correspondent David Chater said the Egyptian government had ordered guards to close the Rafah border by 13:00 GMT on Friday.
Stones were hurled at Egyptian guards by Palestinians after they raised batons and shields and formed a human wall close to one of three crossings.
Witnesses said guards then beat some Palestinians with clubs and fired several shots in the air.
The move has triggered fears among Palestinians, who have been flocking into Egypt for three days for essential supplies following Israel's blockade of the Gaza Strip, that their access to Egypt was about to be closed.
Al Jazeera's Amr El-Kahky said: "Security forces aim to seal two of the three crossings ... one will stay open, but will direct one way traffic - out of Egypt.
"Tension seems to be rising ... because the prospect of the borders closing again, and the Palestinians going back into the so-called prison that is Gaza, is very frightening for them."
He said: "The government took heavy criticism from the West over the border opening.
"The United States congress has already suspended $100 million of aid to Egypt due to the border breach."
David Chater, reporting from Jerusalem, said he believed the closure was a result of Washington putting pressure on Egypt.
He said: "Hosni Mubarak [the president], says that the crossing will be closed today.
"He has come under pressure as to how he dealt with this situation, and I think that the attempt to push the Palestinians back into Gaza is a direct response to US pressure in particular."
He said that the Israeli military establishment had expressed dismay that the border with Egypt had been opened.
He said: "The tight blockade will continue, wth Israel allowing the transfer of limited supplies into the Gaza Strip.
"There is now word coming out that Hamas security forces will assist Egyptian security in closing the Rafah crossing. The Palestinian Authority has also said that they are prepared to handle the situation."
The issue has now turned into a political row between Egypt and Israel.
Matan Vilnai, the Israeli deputy defence minister, said Israel gradually wants to relinquish responsibility for Gaza, now that the territory's border with Egypt had been blown open.
Egypt has angrily rejected the suggestion and said it would not change border arrangements.
The blasts that made holes in Gaza's border with Egypt came after the Israeli government blocked fuel and aid shipments into Gaza beginning last week.
Hamas officials have denied ordering the explosions that blasted open the border walls.
At the World Economic Forum convened in Davos, Switzerland, Salam Fayyad, the Palestinian prime minister whose government is based in the West Bank and has no control over Gaza, called the Israeli blockade of the Gaza Strip "absolutely disastrous".
"This is a pressure cooker kind of situation and a very damaging situation - one that threatens to spiral out of control," he told delegates.
A series of Israeli air raids on Gaza over the past 10 days also claimed the lives of more than 40 Palestinian people, most of them fighters.
Israel says its actions are aimed at halting rockets fired into southern Israel from Gaza by Hamas fighters and denies that it is engaging in "collective punishment" against the Palestinian people.