Witnesses said the protesters also chanted anti-US slogans as they left the headquarters of Jamaat-e-Islami, the country's largest religious party, and marched about one kilometre to hold a demonstration at the tomb of Muhammad Ali Jinnah, the founder of Pakistan.
The rally on Wednesday was organised by Pakistan's powerful religious alliance Muttahida Majlis-e-Amal (MMA), which called it a prelude to countrywide demonstrations expected on Friday.
"These demonstrations will not stop unless the US apologises and punishes the American soldiers responsible for the desecration of the holy Quran," MMA vice-president Ghafoor Ahmed told the participants of the rally.
The demonstration follows mass protests around the world after a 2 May report in Newsweek magazine that US investigators had found that interrogators at Guantanamo threw a Quran in a toilet to humiliate Muslim inmates.
"These demonstrations will not stop unless the US apologises and punishes the American soldiers responsible for the desecration of the holy Quran"
Fifteen people died in Afghanistan as violence erupted there.
The magazine last week retracted the story after its source developed doubts, and the Pentagon has said its own investigation has found no evidence to support the allegation that Qurans were defiled at the prison.
Still, Pakistan has said it will raise the issue with visiting US Assistant Secretary of State Christina Rocca, who started a three-day visit of Pakistan on Wednesday.