The authorities used tear gas and water cannon to disperse the demonstration.
The protest was part of a nationwide rally called by Jamaat-e-Islami, Pakistan’s largest Islamist party.
Charlie Hebdo featured a cartoon of Prophet Muhammad this week, a week after two gunmen carried out a massacre at its offices.
Twelve people were killed in the Paris attack, carried out by two French Muslims angry over earlier depictions of Muhammad in the magazine.
On January 15, Pakistani politicians passed a motion condemning Charlie Hebdo for publishing the latest cartoon.
Religious leaders openly called for journalists at the magazine to be hanged, and several religious groups called for protests after Friday prayers.
In Karachi, at least three people were injured during the clashes between police and about 200 protesters, who were mostly student activists from Jamaat-e-Islami.
Three people were reportedly hurt in the clashes, though it was not clear how they sustained their injuries.
One of the injured has since been confirmed as Asif Hassan, a photographer for the news agency AFP.
He was shot in the chest but doctors say he is out of danger following surgery.
Pakistan has denied firing bullets at the protesters, claiming the police only fired shots into the air.
The protesters had tried to get inside the French consulate.
Protest leaders said they wanted to hand a written complaint to consulate officials, but were stopped by police near the main entrance.
Witnesses say the police used batons, water cannon, tear gas and shooting in the air to disperse the protesters.
The area is now quiet, and protesters have been forced away from the consulate.
Pakistan also erupted in protests in 2006 over publication by a Danish newspaper of cartoon images of Muhammad.
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