One person was killed in Alexandria and another in Damietta province when clashes there erupted between protesters and supporters of Morsi, medics said.
AFP correspondents in Cairo said protesters rallied in the upscale suburb of Maadi following the weekly Friday Muslim prayers.
Official media said smaller protests erupted in the afternoon in several provinces across the country.
The protests come a day after Interior Minister Mohammed Ibrahim survived a bomb targeting his convoy in which 21 people were injured. One of them died of his injuries today, a health official said.
The Islamist Anti-Coup Alliance led by Morsi's Muslim Brotherhood called for Friday's protests but only managed to attract several thousand supporters unlike past rallies when hundreds of thousands showed up.
The dwindling number of protesters come as police have pressed a crackdown on the Brotherhood, arresting hundreds of its members including its supreme guide.
The security forces stormed two major pro-Morsi protest camps on August 14, in an operation that saw hundreds of people killed.
Morsi was ousted by the military on July 3 after popular protests against his single year of turbulent rule. He is being held at an unknown location.