The demonstrations started after Friday's midday prayers and gave religious leaders a platform to criticise General Pervez Musharraf, the Pakistani president, and his government's close relations with the US.
Maulana Fazal-ur Rahman, an opposition leader who led the Islamabad protest, said: "America is the killer of humanity, and we will keep raising our voice against it, and its supporter [Musharraf]."
Peaceful protests were held in the southern city of Karachi, Peshawar in the northwest and the eastern city of Lahore.
Before the protests, police detained dozens of activists and leaders from a radical coalition of six parties: Mutahida Majlis-e-Amal (MMA), or United Action Forum.
The most prominent person detained was the MMA's leader, Qaazi Hussain Ahmed, who was barred from leaving the headquarters of his Jamaat-e-Islami party in Lahore.
Last week, a rally in the city left three people dead, while several shops and buildings were burned by the crowd.