The protesters, some waving Turkish and Armenian flags, marched down the street where reports say the prominent journalist was shot three times as he left his office at the "Agos" newspaper.
One crowd member told Reuters, "(Dink) was an intellectual who loves Turkey and tries to do a lot of things for Turkey, a man who tries to build friendship bridges between communities. We lost one of our brave hearts."
Dink often angered Turkish nationalists with his criticism of mass killings of Armenians by Turks in the early 20th century. Such criticism is a crime in Turkey, and Dink had faced a series of court cases for his outspokenness, including a conviction for insulting Turkish identity in 2005.
He also had said he received numerous death threats before his murder, and he wrote in his last newspaper column that he was so worried about attacks that his head swiveled like a pigeon's as he moved around Istanbul.
Turkey, already in an uphill battle to join the EU, now faces even more pressure.
The first EU official to publicly comment on the killing was Enlargement Commissioner Olli Rehn, who urged Turkey to bring the culprits to justice.
"I am deeply shocked and saddened by this brutal act of violence," Rehn said. "Hrant Dink was a journalist, a respected intellectual who defended his views with conviction and who campaigned for freedom of expression and an open society in [Turkey.]"
The Armenian issue has been a key part of the debate surrounding Turkey's EU bid. In 2006, France's National Assembly passed a bill to make it a crime to deny the massacre was genocide, in a move strongly condemned by Ankara.
Turkish Prime Minister Recep Tayyip Erdogan appeared to allude to the French genocide bill in remarks made on Friday following Dink's assassination.
"Unfortunately, dark hands have chosen Hrant Dink this time to achieve their felonious purposes," Erdogan said. "It is very meaningful that this murder happened when, especially in some countries, the so-called Armenian genocide is at the top of the agenda."
'A Cowardly Act'
The media freedom group Reporters Without Borders called on Turkey to bring the culprits to justice, saying the case will be an important test in Turkey's efforts to join the EU.
Armenian Foreign Minister Vartan Oskanian condemned the murder, saying Dink had lived his life in the belief that there could be understanding, dialogue, and peace among peoples.
And in Washington, the State Department expressed concern over Dink's shooting, while Miklos Haraszti, the OSCE representative for media freedom, condemned it as a cowardly act resulting in tragic loss.
Turkish media reports said as many as eight people had been detained in connection with the killing.
But Western news agencies today quoted Turkish Interior Minister Abdulkadir Aksu as saying that no suspects remain in custody. They also quote Istanbul's governor as saying that authorities have enough evidence to solve the case.