Updated at 4:05 p.m. ET: CAIRO -  Mohammed Morsi, the Muslim Brotherhood-backed candidate, was declared Egypt’s first Islamist president on Sunday with 51.7 percent of last weekend's run-off vote, defeating Ahmed Shafiq, who had been tapped as prime minister by former President Hosni Mubarak.

In an address to Egyptians late Sunday night, Morsi reiterated his platform of unifying all Egyptians. Of those who died while protesting more than a year ago, he said, "Their blood will not go in vain."

Morsi becomes Egypt’s fifth president, following Mubarak, who was president for nearly 30 years before mass protests across the country forced him to resign in February 2011.

The announcement by the state election committee Sunday touched off a jubilant celebration in Cairo's Tahrir Square, where tens of thousands of Brotherhood supporters had gathered in 97-degree heat. The crowd waved national flags and chanted "Allahu Akbar!" or "God is great!"

Morsi will be sworn in on July 1, according to the election timetable.

His victory followed speculation about backroom deals and suspected interference by the ruling military council in determining the outcome in favor of Shafiq, Mubarak’s prime minister.

In his speech Sunday night, Morsi said that contrary to popular belief, he was grateful to the police, whom he called his "brothers and children." He said he would rely on them to maintain "security from the inside."

Daniel Berehulak / Getty Images

Supporters of Mohammed Morsi, the Muslim Brotherhood's candidate, protest against Egypt's military rulers in Tahrir Square on Saturday.

Morsi, who received an engineering degree from the University of Southern California in the early 1980s according to media reports, was a last-minute candidate, chosen to represent the Brotherhood after their preferred choice was disqualified.

On the campaign trail, he promised to institute Islamic law. One of his supporters, cleric Safwat el-Hegazy, issued a direct challenge to Israel, calling for a Muslim super-state across the Middle East with Jerusalem as its capital.

Morsi, 60, distanced himself from the cleric’s comments, but they trailed him on the campaign despite his assertion that he will respect international treaties, including the 1979 peace accord, on which much U.S. aid depends. He said he will not, however, meet with Israeli officials, according to the BBC.

He has also pledged to form an inclusive government to appeal to the many Egyptians, including a large Christian minority worried about potential religious rule. He has repeated that he would maintain his independence from the Brotherhood and not turn Egypt into a theocracy.

Morsi won the first round ballot in May with less than a quarter of the vote.

There were some isolated scuffles in parts of Cairo between rival groups on Sunday. Several hundred Shafiq supporters in the middle-class suburb of Nasr City chanted "Save Egypt! The Brotherhood will destroy it!'' while soldiers tried to keep traffic moving.

The military council will retain control of the biggest army in the Middle East, whose closest ally is the United States. 

Field Marshal Hussein Tantawi, who heads the military council that has ruled Egypt for more than 16 months, congratulated the Muslim Brotherhood's candidate after his presidential election win was confirmed, state television reported. The report, made in a brief headline, did not give further details.

Morsi "will likely face foot-dragging and perhaps outright attempts to undermine his initiatives from key institutions," Elijah Zarwan, senior policy fellow at the European Council on Foreign Relations, said in Cairo. "Faced with such resistance, frustration may tempt him fall into the trap of attempting to throw his new weight around. This would be a mistake. His challenge is to lead a bitterly divided, fearful, and angry population toward a peaceful democratic outcome, without becoming a reviled scapegoat for continued military rule."

Egypt's ruling armed forces were on alert on Sunday as fears of violence mounted in the final hours before the state election committee named the winner.

Sunday's result -- 500 days after the overthrow of Hosni Mubarak -- is historic for the Middle East, but will not end power struggles between the army, Islamists and others over Egypt's future.

The generals, who oversaw Mubarak's departure, have repeatedly said, both to Egyptians and to their close U.S. ally, that they will return to barracks and hand over to civilian rule. But they present themselves as guardians of Egypt's security and long-term interests and moved to block the Islamists from taking more than a share of power.

The military has held power in Egypt for nearly 60 years since the revolution to overthrow a dynasty.

Iran's Foreign Ministry congratulated Egyptians on Sunday for Morsi's victory, saying Egypt was in the final stages of an "Islamic Awakening."

Israeli Prime Minister Benjamin Netanyahu’s office released a statement saying he "appreciates the democratic process in Egypt and respects its outcome."

"Israel expects continue cooperation with the Egyptian administration on the basis of the peace accord between the two countries, which is in the interest of the two peoples and contributes to regional stability,'' the statement said.

The son of a peasant farmer, Morsi has spoken of a simple childhood in a village in the Nile Delta province of Sharqia, recalling how his mother taught him prayer and the Koran. He obtained his doctorate from the University of Southern California in 1982 after studying at Cairo University. 

Following his studies in the United States, he returned to Egypt in 1985. Two of his five children hold U.S. citizenship. 

Charlene Gubash, NBC News producer in Cairo, msnbc.com's Isolde Raftery, Reuters and The Associated Press contributed to this report.

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