Mohammed Mursi is Egypt's first freely elected president

Muslim Brotherhood's Mohammed Mursi on Sunday won the historic post-Mubarak presidential polls in Egypt, beating his rival and former Prime Minister Ahmed Shafiq to become the country's first freely elected president.

Supreme Presidential Elections Commission head Farouq Sultan announced that Mursi had won the presidential run-off.

Mursi, 60, won 51.73 per cent of the vote, beating his rival Shafiq, the Higher Presidential Election Commission said.

Sultan said the election commission had upheld some of the 466 complaints by the candidates, but that the election result still stood.

The announcement prompted scenes of jubilation in Cairo's Tahrir Square, where Mursi's supporters gathered.

Thousands of Muslim Brotherhood supporters had packed Cairo's iconic Tahrir Square in anticipation of a win for their candidate, waving flags and chanting pro-Mursi slogans.

Some schools and shops closing early and people rushed home amid fears of unrest after the result.

Extra troops and police were deployed across Cairo as military helicopters hovered above the city.

The road leading to parliament was shut to traffic, and security measures were in place to protect vital establishments.