The Tahrir Square protest, dubbed "Friday of protecting the revolution," was organized by the Muslim Brotherhood, BikyaMasr.com reported.
Protesters called for the end of military rule in the country and denounced former head of intelligence Omar Suliman's decision to join the presidential race.
Suliman was vice president during Mubarak's last days in power before a violent uprising forced his ouster in February 2011.
Protesters also called for the nominations of other regime affiliates who joined the race to be voided. Pictures of Suleiman, Amr Moussa, who was the minister of foreign affairs for 10 years during Mubarak's reign, and Ahmed Shafiq, Mubarak's last prime minister, appeared around the square with captions such as, "The revolution enemies will not govern."
Muslim Brotherhood leaders took the opportunity to promote their nominee in the presidential election, Khairat al-Shater.
The protest came a day after Egypt's Parliament passed a bill forbidding certain senior officials of the former regime from running for president, Haaretz reported.
Under the proposed law, anyone who served as prime minister, vice president or the head of a party in the 10 years preceding the revolution will not be allowed to run for president in the next 10 years.
The bill would block Suliman and Shafiq from participating in the election but Moussa would still be eligible.
The ruling military council will have to approve the bill before it can become law.
Egypt's presidential elections are scheduled May 23-24. If no candidate takes more than 50 percent of the votes in the first round, a round of runoff elections will be conducted in June.