Adding to the uncertainty, Hamdeen Sabahi called for a partial vote recount, citing violations that he claimed could change the outcome, a prospect that may further inflame an already explosive race. Sabahi, a socialist and a champion of the poor, came in third by a margin of about 700,000 votes, leaving him out of the next round to be held on June 16-17.
Many Egyptians were dismayed by the early results, which opened a contest that looked like a throwback to Mubarak's era - a rivalry between a military-rooted strongman promising a firm hand to ensure stability and Islamists who were repressed under the old regime but have become the most powerful political force in post-revolutionary Egypt.
Each candidate has die-hard supporters but is also loathed by significant sectors of the population.
The first round race was tight. Preliminary counts Friday from stations around the country reported by the state news agency gave Morsi 25.3 percent and Shafiq 24.9 percent with a less than 100,000-vote difference. The election commission said that about 50 percent of more than 50 million eligible voters turned out for the first round, which had 13 contenders.
A large chunk of the vote - more than 40 percent - went to candidates who were seen as more in the spirit of the uprising that toppled Mubarak, that is neither from the Brotherhood nor from the so-called feloul, or "remnants" of the old autocratic regime.
Sabahi came in third with a surprisingly strong showing of 21.5 percent, followed by Abolfotoh, a moderate Islamist who broke with the Brotherhood.
Steven Cook, an Egypt expert with the Council on Foreign Relations, a U.S. think tank, said the outcome of the battles between the two extremes is hard to predict.
"Egypt is following the classic pattern of revolutions. People who made them get frozen out," he said.
He said Shafiq would rely on the same "dynamics" of fanning fears of the Islamists that Mubarak relied on in the past. On the other hand, the Brotherhood will play on the fear of Shafiq's re-creating the old regime.
"I am fed up with being labeled 'old regime,' " Shafiq said at a news conference in his campaign headquarters in Cairo. "All Egyptians are part of the old regime."
In an effort to broaden his support, Morsi met with public figures and political groups Saturday, and tried to present himself as the candidate for all Egyptians. But in a sign of the tough task ahead for the Brotherhood, three of the presidential candidates, including Sabahi, didn't turn up.
The Brotherhood won close to 50 percent of the seats in parliament in the country's first parliamentary elections in the post-Mubarak era. But the fundamentalist group's credibility has taken a hard hit since because of the legislature's performance and the Brotherhood's reneging on a string of public pledges - including not to run a presidential candidate.