Muslim Brotherhood presidential candidate Mohamed Morsi has been named Egypt's fifth president after narrowly defeating his rival, Mubarak-era PM Ahmed Shafiq, in the hotly-contested presidential elections' runoffs. His victory, however, is barely expected to bring immediate stability to the turmoil-hit country.

The final results, which gave 52 per cent of the vote to Morsi, were announced around 4:30pm, Sunday, at the Cairo headquarters of the Supreme Presidential Electoral Commission (SPEC).

The announcement sparked massive celebrations in Cairo's Tahrir Square, the epicentre of Egypt's uprising.

Morsi won 13,280,131 votes against 12,347,380 (a bit over 48 per cent) for Shafiq, according to the SPEC's official vote count, announced after allegations of electoral fraud – filed by both candidates' campaigns – were declared.

The total number of registered voters in Egypt stands at 50,958,794. Voter turnout in the presidential runoff was 26,420,763 (nearly 52 per cent). The total number of valid ballots cast was 25,575,511, while the number of voided ballots was 843,252.                                           

"I would like to thank the military council, the judicial system and the police for their efforts in making the elections clean and fair," Morsi campaign manager Ahmed Abdel-Atti said shortly after the announcement.

Morsi, who resigned as head of the Brotherhood's Freedom and Justice Party (FJP) shortly after the result announcement, launched his presidential campaign after Brotherhood second-in-command Khairat El-Shater was disqualified from the race by Egypt's electoral commission in April. El-Shater was eliminated due to a prior criminal conviction under the Mubarak regime.

Morsi's win in Egypt's first-ever genuine multi-candidate presidential election puts an end to a 60-year military monopoly on the office of president. His predecessors, who ruled the country since the 1952 Free Officers' coup – Mohamed Naguib, Gamal Abdel-Nasser, Anwar El-Sadat and Hosni Mubarak – all came from within the army's ranks.

However, Morsi's victory does not mean that the military will loosen its current grip on power. Recent decisions by the Supreme Council of the Armed Forces (SCAF) give the military junta expanded authorities at the expense of both parliament and the office of the presidency.

State above the state?

The SCAF released late on Sunday 17 June an addendum to the military-authored March 2011 Constitutional Declaration, giving the SCAF complete independence as Egypt's military institution, and magnifying its political authorities, critics say.

The articles of the amended Constitutional Declaration put the SCAF in sole charge of the armed forces and its affairs, including selecting military leaders including the defence minister. The president will also not be able to declare a state of war or order the deployment of troops, even to contain domestic disturbances, without the military council's consent, according to the terms of the constitutional addendum.

Politically, the SCAF has the authority to appoint a new Constituent Assembly tasked with drafting a new constitution, should the current assembly be dismantled.

"[The addendum] means that the SCAF has become a state above the state, with wide legislative and executive powers, a veto on constitutional and other political matters, and stands immune to any challenges," liberal political analyst Amr Hamzawy  said via Twitter, halfway through the initial vote count on 17 June, which also indicated a Morsi win.

The current Constituent Assembly was elected last Tuesday by Egypt's parliament, but could well be dissolved after the People's Assembly (the lower house of Egypt's parliament) was made defunct by the SCAF, pursuant to a court ruling that declared a parliamentary election law – which regulated last year's legislative polls – unconstitutional.

The dissolution of parliament's lower house means the SCAF now boasts full legislative and executive authority until a new People's Assembly can be elected.

The SCAF, however, played down the importance of the controversial constitutional document and its legislative powers, saying that the authority of the new president – to whom the military council will relinquish power upon the official announcement of results – will remain untouched.

"The president-elect will assume all the president's rightful powers," said SCAF member General Adel El-Assar at an 18 June press conference. "The legislative [authorities] that the [military] council have are only for a limited period, until a new People's Assembly is elected."

Revolutionary author Alaa El-Aswany had earlier tweeted: "The Constitutional Declaration is a complete turn against the revolution and it makes the president a mere affiliate of the military council and extends the transitional period indefinitely."

El-Aswany added: "The Constitutional Declaration blows up the core of democracy. While we object to the fact that the Brotherhood is forming the Constituent Assembly, letting the military council do so is no solution at all."

The SCAF assumed power on an interim basis on 11 February 2011 right after the overthrow of Mubarak, who remained in power for 30 years. The military forced his resignation after 18 days of countrywide protests on 11 February 2011.

Egypt's 2012 presidential elections were the second multi-candidate poll in the country's history. The first multi-candidate presidential poll took place in 2005 and saw then president Mubarak secure a clear victory, which many observers put down to massive vote-rigging by the now-defunct National Democratic Party (NDP).