But a conflict already emerged Sunday.
Saad el-Husseini, of the executive bureau of the Muslim Brotherhood's Freedom and Justice Party confirmed the president-elect would take his oath of office before Parliament, not before Egypt's High Constitutional Court, Ahram Online reported.
The lower house of Egypt's Parliament was dissolved by the ruling military council, and the constitutional court ruled that the new president must be sworn in before the court, not the Parliament.
But the report said Morsi's oath before the court would imply acceptance of the dissolution of Parliament. The Muslim Brotherhood strongly opposed the dissolution, Ahram Online said.
Tens of thousands of Morsi's supporters in Cairo's Tahrir Square cheered shouts of jubilation Sunday afternoon seconds after Farouq Sultan chairman of the Presidential Election Committee made the announcement.
Morsi's win puts an end to the country's 60-year military monopoly of presidents, Ahram Online said, noting all his predecessors rose from the army's ranks.
Sultan said Morsi's opponent, former prime minister Ahmed Shafiq, won more than 12 million votes constituting 48.27 percent; and Morsi 51.73 percent with more than 13 million votes. He said the turnout for the second presidential runoff was some 51 percent.
The thousands of Morsi's supporters who rallied in Cairo's Tahrir Square and Shafiq's supporters who rallied in Nasser City in Cairo waited tensely for the results as Sultan delivered an hourlong speech that was televised throughout the world. The speech detailed the entire electoral process of each region and the work conducted by the commission, whose members were faced with having to investigate multiple allegations of election rigging and forgery.
Fearing possible violence, shortly before the election results were announced, the Supreme Council of the Armed Forces issued a warning, saying it would treat anyone seeking to challenge the result "with an iron fist."
Egypt's Interior Ministry issued a statement saying it would not tolerate any turmoil and said police forces had been given orders to shoot to kill anyone who attempts to attack the police after the results are delivered, CNN reported.
Notable deaths of 2014 [PHOTOS]