From there they were taken through Israel to the Erez terminal in the northern Gaza Strip, the Israeli military said.
Reporters at the scene said the Palestinians began crossing back into Gaza through Erez.
The Erez crossing is a long bus ride away from Rafah, where most of the Palestinians were waiting.
Earlier on Sunday, Al Jazeera reported quoting Egyptian security sources that about 102 Palestinians would cross into Gaza through Awja.
Hamas has criticised the plan, saying it increases Israel's control over Gaza.
Both Israel and Egypt have rejected demands by Hamas to have partial control of the Rafah crossing.
Alan Fisher, reporting for Al Jazeera from the Erez crossing on Sunday, said: "Initially there was a plan to bring the people who've been stranded [in northern Sinai] through Kerem Shalom but Hamas reportedly said that if that happened they would shell the area ... .
"That's why they've decided to bring the people in buses all the way north to Erez."
A security source said Israel and Egypt were negotiating to arrange for the remaining registered Palestinians to go home.
Some say the process was made easier for supporters of the governing Fatah party of Mahmud Abbas, the Palestinian president, while Hamas members were not even being allowed to register.
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Many of those left behind say they have been barred for their political beliefs.
They said they were not allowed to register because they were supporters of Hamas, the Islamic movement.
Ibrahim Abul Naja, a member of Fatah's supreme council in Gaza, said the party was not happy about the option of letting stranded Palestinians on the Egyptian side to cross through the Awja terminal.
But he denied accusations that Fatah supported the closure of crossings into the Gaza Strip.
Nour Odeh, Al Jazeera's correspondent in Gaza, said: "This is not an arrangement that any Palestinian party is happy with, including Fatah [Hamas's rival]."
Al Jazeera quoted medical sources as confirming that one of the stranded Palestinians had died on the Egyptian side of the Rafah terminal.
Around 6000 Palestinians, including women, children and sick and elderly people, remain stranded at this crossing.
The stranded Palestinians have been running short of food, medical care and basic amenities since the border terminal shut a month and a half ago.
More than 10 people have died in this period.