"We are at the pavement where they tried to clean his blood with soap," Dink's wife Rakel said in a speech from the office balcony.
"You are here for justice today. A scream for justice rises from your silence."
The crowd held a minute's silence at mark the moment when Dink was shot.
Many in the crowd held black-and-white placards that read "For Hrant, For Justice" in Turkish, Armenian and other languages.
"The killer state will be called to account," some chanted.
"I can see that justice has not been done and it makes me angry," said Ulas Arikan, an advertising executive who was at the protest. "But I believe if we raise our voices justice will be achieved."
There was also some violence at the demonstrations as some protesters clashed with police.
Ankara has vowed to prosecute all those responsible for Dink's killing and 19 suspects are on trial, with the next hearing due on February 11.
"There is no doubt that article 301 contributed to intellectuals being targeted, and some, like Dink, have paid the highest price"
from rights watchdog Bia2
Although the chief suspect confessed to his murder, many press commentators believe the police enquiry was deliberately flawed to hide the true instigators.
According to a court indictment, one of the defendants in the Dink case acted as a police informer and told the police of plans to assassinate Dink in the months before the murder.
On Friday, rights group Amnesty International urged Turkey to widen the investigation into his death and the media called for the alleged complicity of security officials to be fully examined.
Dink had recieved a number of death threats over his writings.
His work also brought him a suspended 6-month jail sentence under Turkey's article 301, a law that makes it a crime to insult Turkish identity.
The law has been used to prosecute a number of writers, like Dink, who have written about Turkey's role in the mass killings of Armenians by Ottoman Turks and Kurds in 1915.
Erol Onderoglu, from the human rights watchdog Bia2, said: "There is no doubt that article 301 contributed to intellectuals being targeted, and some, like Dink, have paid the highest price."
Ankara has been unwilling to scrap the law, but in November last year, suggested a revision of the law would soon be bought before parliament.
Turkey has come under pressure from the EU to change the law, which the European bloc sees as an obstacle to free speech and Turkey's goal of obtaining EU membership.