The Islamist Anti-Coup Alliance urged its supporters to stay away from the iconic square during the protests to avoid more bloodshed after a week in which nearly 80 Egyptians were killed, many of them in the capital.
The interior ministry warned the Islamists that it will "confront any attempts to break the legitimacy" of the interim government.
Some 2,000 supporters of deposed president Mohamed Morsi rallied outside a presidential palace, carrying posters of the bearded leader now detained by the military after it removed him on July 3.
An interior ministry statement said most of the "limited" marches passed off without incident.
But in Sinai, where Islamist militants are waging an insurgency against security forces, at least nine soldiers were wounded when improvised bombs targeted their vehicles in the border town of Rafah, a security official said.
The Anti-Coup Alliance, which rejects Egypt's military-installed government, had called on protesters in a last-minute statement to avoid marching on Tahrir Square.
The "coup regime is shedding blood without any respect to law or values adopted by our great people" said the coalition, spearheaded by Morsi's Muslim Brotherhood movement.
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