Monday's rally began in the afternoon to commemorate people killed in clashes with security forces two years ago, then turned into chanting against General Abdel Fattah al-Sisi, whose forces toppled Mursi in July.
Army and police who had been stationed by armored personnel carriers after sealing off Tahrir melted away by the time the protesters arrived at the square, the heart of the 2011 popular uprising that ejected autocrat Hosni Mubarak.
"A word in your ear, Sisi, don't dream of being my president!" the protesters yelled. It was not clear why army and police units made no attempt to stop the demonstrators.
The general has emerged as a popular figure among many Egyptians pleased to see the end of Morsi's administration. Many analysts believe he would likely win a presidential election due next year were he to run.
But some Egyptians are opposed both to Mursi's Muslim Brotherhood and the current military-steered government, and they dominated the Tahrir Square rally.
On Saturday, a Muslim Brotherhood-led coalition offered holding negotiations to put an end to deadly turmoil across the country.
The coalition of Islamic parties has also called on all political parties and patriotic figures as well as revolutionary forces to enter discussions to end the ongoing crisis.
NTJ/BA