- NEW: Ex-Mubarak premier Shafik's headquarters is set ablaze
- NEW: "Where is the revolution?" protesters chant in Tahrir Square
- Shafik will face Muslim Brotherhood candidate Morsi in June 16-17 runoff
- The winner will be Egypt's first freely elected president
Cairo (CNN) -- New protests erupted in Egypt's capital after news that ousted strongman Hosni Mubarak's former premier will face off against a representative of the Muslim Brotherhood in the country's presidential runoff.
In Tahrir Square, several thousand protesters called on Egyptian courts to disqualify former Prime Minister Ahmed Shafik, chanting, "Where is the revolution?" Others ransacked Shafik's campaign headquarters and set it ablaze after learning that he was one of the two candidates who made it through the first round of voting.
Shafik campaign spokesman Ahmed Serhan said the fire was soon contained and no one was injured. Serhan said that while the anti-Shafik protesters numbered in the dozens, "Supporters in the hundreds are outside the building supporting him."
In Tahrir Square, the epicenter of the 2011 revolt, the crowd carried Khaled Ali -- a presidential candidate who failed to make the runoff -- on their shoulders while demanding an end to the military government that followed Mubarak. Anti-Shafik protests were also reported in Alexandria and other cities, and revolutionary leaders said they would hold more on Tuesday outside Egypt's High Court of Justice.
The June 16-17 runoff will pit Shafik against Muslim Brotherhood candidate Mohamed Morsi, Farouk Sultan, head of Egypt's Election Commission, told reporters Monday in Cairo. Morsi received 5.7 million votes, followed by Shafik's 5.5 million, according to the commission.
Voters' dilemma: Choice between two tyrants?
In all, 23 million of Egypt's 50 million eligible voters, or 46%, cast ballots in the first round of the election.
Thirteen candidates appeared on the first-round ballot, though two withdrew from the race after ballots were printed. The winner of the landmark vote will become Egypt's first freely elected president.
Neither of the frontrunners had been favored by the revolutionaries responsible for toppling Mubarak.
Morsi is an American-educated engineer who has promised to stand for democracy, women's rights and peaceful relations with Israel if he emerges as the victor. Still, he's an Islamist figure who has argued for barring women from the Egyptian presidency and called Israeli leaders "vampires" and "killers."
Though the Brotherhood played little role in the revolution, its well-honed political machine succeeded in getting its supporters to the polls. Meanwhile, many of those who faced down the Mubarak regime at Tahrir Square did not follow up with the political organizing that would have been needed to gain electoral victory.
Shafik, a former air force officer with close ties to Egypt's powerful military, has attempted to distance himself from Egypt's deposed leader. He told reporters last week that there's "no going back" to the Mubarak years.
Still, he appealed to those who may have had second thoughts about the magnitude of the change that has swept across the country. The uncertainty has had an impact: Last week, the Cairo stock market plunged by 3% in a single day.
Former U.S. President Jimmy Carter, who led a delegation observing the voting, told reporters last week in Cairo that he couldn't say "the entire process has been proper" because of restraints on observers. But the group found the election period to be peaceful, with citizens accepting the voting process as "quite successful."
"There were many violations, and I think each violation is serious. But I think collectively they did not affect the basic integrity of the election," he said.
Carter said there were no apparent patterns in election procedures that "favored a particular candidate."
Mubarak led the North African nation for 30 years before being forced out last year amid a popular outcry that marked one of the seminal developments of the Arab Spring.
Distrust and anger in Egypt, particularly against the military's power in governmental affairs, have inspired continued protests, some of which have been marked by deadly clashes. Many protesters are upset about what they see as the slow pace of reform since Mubarak's ouster. Some are also concerned that the country's military leadership is delaying the transition to civilian rule.
The Supreme Council of the Armed Forces has insisted that it will hand over power to an elected civilian government.
In January, two Islamist parties -- the Freedom and Justice Party with 235 seats and the conservative Al Nour party with 121 seats -- won about 70% of the seats in the lower house of parliament in the first elections for an elected governing body in the post-Mubarak era. The rest of the assembly's 498 seats were divided among other parties.
CNN's Ben Wedeman and journalist Mohamed Fadel Fahmy contributed to this report.
