Police fired stun grenades to disperse protesters who waved Palestine Liberation Organization flags and tried to burn Danish flags, which they laid on the ground.
Two stone throwers were arrested and transferred for interrogation, police said.
Later, dozens of Arab residents of east Jerusalem against stoned police officers to protest the publication of the cartoons published. No injuries were reported but seven suspects were detained.
The publication of caricatures in Denmark and other European countries, including one portraying Mohammad wearing a bomb-like turban, have triggered protests around the globe.
Meanwhile, the Jyllands-Posten editor who commissioned cartoons of the prophet Mohammad that have angered Muslims worldwide has been sent on holiday after suggesting he would print Iranian cartoons of the Holocaust.
The Danish newspaper published the cartoons of Muhammad last September. Muslims consider images of their prophet to be blasphemous and tensions later flared in the Middle East after other European newspapers reprinted the cartoons in the name of free speech.
'Take a vacation'
"The editors have told Flemming Rose to take a vacation because no one can understand the kind of pressure he has been under," Jyllands-Posten editor Carsten Juste told Berlingske Tidende newspaper.
Juste was not available for comment.
The chairman of the foundation that owns the newspaper, Asger Noergaard Larsen, refused calls to sack Juste and Rose, saying he fully backed the management and that there is no crisis at the newspaper.
"I think you could say that the violence in the Middle East and the boycott of Danish goods looks like a crisis, but we do not have a crisis," Larsen told Berlingske Tidende.
Flemming Rose, Jyllands-Posten's culture editor, told CNN on Wednesday he would consider publishing proposed Iranian cartoons of the Holocaust. The newspaper later made a public apology and played down his comments.
"Flemming Rose has expressed regret for his error of judgment that must be ascribed to the fact that, during the past four months, he has experienced inhumanly hard pressure and been besieged by Danish as well as international media almost around the clock," Juste on his newspaper's Website.
"Under no circumstances will we allow ourselves to be latched onto the tasteless media stunt of an Iranian newspaper," Juste said.
Reuters contributed to this report