Mohamed Morsy is the first popularly elected civilian president of Egypt, the official website of Brotherhood's Freedom and Justice Party announced.
The Brotherhood's claim of victory over the weekend in the run-off between Morsy and Ahmed Shafik, the last prime minister during Mubarak's regime, was quickly contested by Shafik's aide saying that the group was hijacking the election.
Our counting of the votes has so far showed that we are ahead with 52 percent of the vote but we refuse to break the law and issue any numbers now, Mahmoud Baraka, the media spokesperson of Shafik's campaign, had said before the Brotherhood's lead was confirmed by a member of the election committee.
The Brotherhood said that with 98 percent of the total ballot count of 24.6 million, Morsy won with 51.8 percent of votes while Shafiq got 48.1 percent.
The election result was yet to be finalized, the unnamed member told Reuters confirming the lead. The final result announcement is not expected until Thursday.
Egypt's military generals, however, have dissolved the parliament and issued an interim constitution which grants the generals the ability to control the budget and determine who writes a permanent constitution.
The Brotherhood's speaker of parliament Saad al-Katatni met with the deputy head of the military council, Chief of Staff, Gen. Sami Anan, Sunday to register the group's protest over the dissolution, according to an AP report.
Al-Katatni said the group didn't accept the military government's decision and that the military was not entitled to issue an interim constitution.
The Islamists and the military, both of which got wider influence and powers after the fall of Hosni Mubarak, have been vying with each other in the run-up to the presidential election. The military generals, who have ruled since Feb 11 last year, ever since the ouster of Mubarak, could potentially debilitate the newly elected president's policies.
At an early morning press conference Monday, declaring their win, the Brotherhood officials looked enthusiastic as they chanted, Down with military rule.
Thank God who guided the people of Egypt to this right path, the path of freedom and democracy, Morsy told the crowd at his campaign headquarters. He promised to Egypt in all its factions, Muslims and Christians that be would be a president for all Egyptians ... a servant to them and seek a civil, democratic, constitutional and modern state, an AP report said.