Morsi will become the first democratically elected civilian to hold the office of president — a symbolic victory in the Muslim Brotherhood's fight for power against the country's military-led government.
The Muslim Brotherhood said in a statement late Sunday that Morsi had resigned his positions in both the Brotherhood and its Freedom and Justice Party, fulfilling a campaign promise.
"I pledge to be a president who serves his people and works for them," Morsi said on his official web page. "I will not betray God in defending your rights and the rights of this nation."
He was scheduled to address the nation Sunday night in his first speech after being declared president.
The commission said Morsi won with 51.7 per cent of the vote versus 48.3 per cent for Ahmed Shafiq, who was the last prime minister under deposed leader Hosni Mubarak.
More than 26 million people voted, with about 800,000 ballots invalidated.
United Nations Secretary General Ban Ki-moon said the election victory marked the "end of one important phase of Egypt's ongoing transition to greater democracy." He also called on Morsi "to strengthen and build strong, independent institutions and to allow civil society to flourish and to play its role fully and freely."
Egyptian-Canadian activist Ahmad Shokr, who purposely spoiled his ballot, said the real question now is "how much power will this newly elected president have?"
Just one week ago, at the moment polls were closing in the runoff election, the ruling generals issued constitutional amendments that stripped the president's office of most of its major powers. They made themselves the final arbiters over the most pressing issues such as writing the constitution, legislating, passing the state budget, and granted military police broad powers to detain civilians.
A few days before that constitutional declaration, a court dissolved the freely elected parliament, which is dominated by the Muslim Brotherhood.
"Key areas of state policy remain in the hands of the generals," Shokr said. "The political arm of the Muslim Brotherhood rejected [those moves] and I hope that they will honour what they said and they'll continue to build concensus with other groups and decide together the shape of Egypt's new civlian democracy."
Women's groups worried
The White House issued a statement through press secretary Jay Carney congratulating Morsi on his victory. The statement emphasized the importance of recognizing the democratic rights of all Egyptians:
“We believe in the importance of the new Egyptian government upholding universal values, and respecting the rights of all Egyptian citizens — including women and religious minorities such as Coptic Christians.
We believe it is essential for the Egyptian government to continue to fulfill Egypt’s role as a pillar of regional peace, security and stability.”
Many women's rights activists are especially worried. Dalia Ziada, a Cairo women's advocate, told CBC News on Sunday that she was "very sad" about Morsi's win.
Ziada had recently been in a meeting with representatives in Morsi's campaign and she is concerned the regime will "try to take actions against people, against human rights and freedoms, by claiming those are orders from God."
"We were speaking with them, with how they see human rights, women's rights," Ziada said. "They said 'we see them according to Sharia' ... and they insisted on speaking on women in biological [terms], not in economic or political terms."
A massive crowd of Morsi supporters in Cairo's Tahrir Square erupted in jubilation, dancing when the result was read out on live television.
In Israel, the office of Prime Minister Benjamin Netanyahu put out a cautious statement saying that Israel "appreciates the democratic process in Egypt and respects the results of the presidential elections."
According to The Jerusalem Post, the statement said Israel "looks forward to continuing cooperation with the Egyptian government on the basis of the peace treaty between the two countries, which is a joint interest of both peoples and contributes to regional stability."
Over in Gaza City, thousands of people are celebrating in the streets with gunmen firing automatic weapons in the air, and mosque loudspeakers blaring prayers. People are handing out candy on street corners. Gaza is ruled by the Islamic group Hamas, a local offshoot of the Muslim Brotherhood that draws inspiration from the Egyptian organization.
Hamas Prime Minister Ismail Haniyeh phoned Morsi to congratulate him on becoming Egypt's first Islamist president.
"This is a victory for all Arabs and Muslims, and this is God's promise to his believers," the Hamas leader said to the newly elected president.
Canadian Foreign Affairs Minister John Baird recognized Egypt's milestone in a statement Sunday night, calling the elections "an important step" toward "a better, brighter future."
Baird urged Egypt to uphold democracy, freedom and human rights and to ensure the rights of women and religious minorities are also protected.
“Canada wishes President-elect Dr. Mohammed Morsi well in working to fulfill the aspirations of all Egyptians," the statement said.
The announcement of the new president puts an end to uncertainty about who is the official winner but promises no resolution to the power struggles between Islamists, the military and other factions in the country.
Many Egyptians have rallied behind Morsi as a chance to finally rid the country of the old Mubarak regime, while others support Shafiq as the best bet to counter Islamists and restore order after a year of protests, economic hardship, and fear about crime and continued instability.
But there is little hope that the results will produce an end to 16 months of political turmoil. A Morsi victory will likely see the new civilian government fight for its authority against a military that has ensured that its powers persist past the transition.