Earlier in the day mourners gathered outside the Agos newspaper office, where Dink was shot, holding identical black-and-white signs reading "We are all Hrant Dink" and "We are all Armenians".
Rakel, Dink's widow, told mourners: "We are seeing off our brother with a silent walk, without slogans and without asking how a baby became a murderer."
White doves were released into the air and much of downtown Istanbul was closed to traffic.
The funeral took place amid tight security as those following the hearse walked the 8km distance from the Agos headquarters to the church where Dink was to be burried.
Turkish media has criticised top politicians and armed forces chiefs for not attending the funeral.
Cengiz Candar, a columnist in a Turkish newspaper, wrote: "If the president, the prime minister and chief of the general staff came to the funeral, I would be hopeful the state has given up on a lynching culture and started to [practice] self-criticism."
"We especially belittle our minorities. We do not consider our citizens of diverse ethnic groups as one of our own. We hate different points of view"
Mehmet Ali Birand,
Dink's murder has stirred debate about nationalism in Turkey and has been viewed with concern abroad, especially by the Armenian diaspora.
Police say Ogun Samast, a seventeen-year-old, has confessed to killing Dink for "insulting" Turks and that Yasin Hayal, a friend of Samast, has admitted that he incited Samast to kill Dink.
Samast is one of seven people allegedly in custody in connection with Dink's murder.
Aykut Cengiz Engin, Istanbul's chief prosecutor, has said that investigators have found no link between Friday's murder and "known ideological or separatist" illegal organisations, but added: "... we are investigating in detail the possibility that it was carried out by an organisation".
Dink had been prosecuted for his views on the massacres of Armenians by Ottoman Turks in 1915, which he called genocide.
He was given a suspended six-month jail sentence, under "Article 301", last year for "insulting Turkishness".
Other writers and intellectuals in Turkey who have expressed the view that Turkey should "face up" to its role in the massacres of Armenians have come under similar criticism from nationalists.
Mehmet Ali Birand, a Turkish commentator, said: "We are all responsible [for Dink's murder]. We especially belittle our minorities. We do not consider our citizens of diverse ethnic groups as one of our own. We hate different points of view."
In recent years Turkey has undergone a number of reforms aimed at preparing the country for EU membership.
A more liberal attitude to national minorities is one of the demands made on Turkey by the EU.
Turkey denies claims that 1.5 million Armenians died in a genocide at Ottoman Turkish hands, instead saying simply that large numbers of both Christian Armenians and Muslim Turks perished.
But many foreign parliaments have passed laws recognising the massacres as genocide.