The Presidential Election Commission announced that Mohammed Morsi, head of the Brotherhood's political front, the Freedom and Justice Party, won a narrow but clear victory. There is no appeal.
Supporters of the Muslim Brotherhood in Tahrir SquareThe declaration by the commission's chairman, Farouq Sultan, a judge close to ex-President Mr Mubarak, relieves immediate concern at the possibility of widespread unrest by Islamists and secular revolutionaries, who had feared the win would be given to Mr Morsi's opponent, Ahmed Shafiq,a retired general and Mr Mubarak's last prime minister.
The Brotherhood's own count of published polling station figures had given Mr Morsi a 52-48 per cent win, a judgement agreed by most independent newspapers and observers. Final election figures from the commission reflected a similar score. Morsi won 13,230,131 votes against Shafiq who clinched 12,347,380.2
In advance of the declaration, troops and police flooded the streets of the capital to protect public buildings in case of disorder. The army had threatened a "firm response" to any sign of trouble.
The result is a remarkable achievement for the Islamists, who emerged from decades of persecution to seize a seemingly unassailable position in Egypt's politics after the overthrow of Mr Mubarak. A month ago, they were in control of the first freely elected parliament, were set to dominate the comittee drawing up a new constitution, and their candidate had led the first round of voting in the presidential elections.
Supporters of Mohammed Morsi in Tahrir SquareFollowing recent decrees, the military interim rulers, the Supreme Council of the Armed Forces (SCAF), dissolved parliament following a separate ruling by Mr Sultan in his other role as head of the constitutional court, reserved its powers to itself, and gave itself a veto over any new constitution.
Amid rumours that the result yesterday was in part the result of negotiations with the army to co-operate in the future government of Egypt, the Brotherhood must now decide how hard to push for full powers to be returned to the president's office.
In the near future, it is likely that Mr Morsi, who retains the right to appoint a prime minister and cabinet, will retain considerable authority over domestic policy, while the army directs security, defence and foreign policy.
That is a worst-case scenario for secular liberals who fear the growing Islamicisation of society and at the same time will have little relief from the army's often repressive policing of protest.
Mr Morsi will be chairman of the National Defence Council - but decisions will be taken by a majority vote, the SCAF has decreed, and 11 of the 16 members will be generals.
This means, among other things, that there is likely to be little immediate change in the policy of military co-operation with the United States and no change to the peace treaty with Israel.
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