Egypt's electoral commission says a presidential runoff next month will pit the Muslim Brotherhood's candidate, Mohamed Mursi, against Ahmed Shafiq, ousted President Hosni Mubarak's last prime minister.
Commission chief Faruq Sultan said Mursi won 5.76 million votes, while Shafiq garnered 5.5 million votes.
The commission put the official turnout in the presidential vote at 46 percent of the 50 million Egyptians who were eligible to vote.
Sultan has denied allegations of fraud raised earlier hours ahead of the results announcement by two candidates who did not qualify for the runoff.
Twelve candidates competed in the election, which came more than one year after Mubarak was ousted during mass demonstrations in February 2011.
The Supreme Council of the Armed Forces, in power since Mubarak's downfall, has pledged to restore civilian rule by the end of June.
The vote has left Egypt deeply divided. Many Egyptians worry that a win by Shafiq could lead to a revival of the Mubarak regime.
Hundreds of people took to the streets in Cairo and Alexandria on May 28, unhappy with Shafiq qualifying for the runoff. State media reported that some 500 people gathered in Tahrir Square in Cairo, chanting: "For the second time, people want to oust the regime."
Shafiq pleged on May 26 to work to consolidate progress in the wake of the country's "Arab Spring" revolution, which was spearheaded by young people, if he is elected.
He told a gathering of young people in Cairo that "there is no going back."
"I'm stretching my hand out to all Egyptians, I accept all dialogues with all politicians from all forces," Shafiq said. "At the same time, I'm insisting on rallying to the people's side and I'm inviting you all to make deals with people."
If Mursi, a conservative Islamist, wins, the Muslim Brotherhood would be in position to exert even greater control over state institutions, as the organization already controls nearly half of the seats in parliament that it won in separate elections earlier this year.
Until a new constitution is approved, however, it is unclear what powers the new president will have. There have been concerns the military may seek to retain some powers even after handing over to a civilian government.
Based on reporting by AFP, dpa, and Reuters