The candidacy of Barghouti, who is seen as the inspiration behind the four-year Palestinian uprising, was presented to the central elections commission by his wife who had earlier visited him in the Israeli prison where he is serving five life sentences.
“I officially presented Marwan’s candidacy for the presidential elections,” Fadwa Barghouti said from the West Bank town of Ramallah barely three hours before the midnight deadline for candidates to register.
Barghouti’s last-minute decision came five days after he announced that he would not be contesting the poll to replace the late Yasser Arafat.
The PLO chairman and official Fatah candidate Mahmud Abbas had been expected to win the January 9 contest easily, but Barghouti immediately became the frontrunner.
Barghouti’s announcement drew a swift condemnation from the Fatah central committee, which reiterated its support for Abbas.
“We regard Marwan’s position as astonishing and reprehensible. It does not conform to the traditions of Fatah,” Tayeb Abdelrahim, a committee member and general secretary of the presidential office said.
Barghouti, who is running as an independent, would “unfortunately have to renounce his membership of Fatah,” he said.
A moderate former prime minister, Mr Abbas is the choice of the Palestinian establishment, but he lacks popular support. In contrast, Mr Barghouti is by far the most popular Palestinian politician after the death of Arafat.
A challenge by Mr Barghouti has the potential to split Fatah — the dominant Palestinian faction founded by Yasser Arafat.
Two cells of the Al-Aqsa Martyrs Brigades, a radical armed group linked to Fatah, criticised Barghouti’s decision to run, calling it divisive.
Meanwhile in Israel, Prime Minister Ariel Sharon faced a political crisis after was forced to sack his main coalition partner, Shinui, after it voted against his budget.
He must now shore up his coalition as quickly as possible to avoid snap elections.
Sharon’s most likely option is to try and form a coalition with the main opposition Labour party and the UTJ, in order to save his government, which has been left with only 40 seats out of 120.
He is expected to try to wrap up a deal by Monday to avoid the risk of being toppled by a threatened no-confidence vote that day.
The premier has been without a majority for nearly six months after traditional right-wing allies were either sacked or quit the coalition in protest over his Gaza withdrawal plan.