The crowd held Friday prayers in the square, which was the epicenter of the uprising that forced longtime leader Hosni Mubarak to step down last year.
The results of the race were delayed amid challenges from Morsi's contender, Mubarak's last Prime Minister Ahmed Shafiq, adding tension to an already explosive political standoff.
The cleric leading the prayers said Mohammed Morsi, the Muslim Brotherhood's presidential candidate, was the clear winner in the election.
Protesters chanted against the military council, which issued a declaration last week stripping the next president of much of his authority.
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