Muhammed Wisam Sankari went missing on 23 July after leaving his home in the conservative Fatih district.
Sankari arrived in Istanbul a year ago after fleeing the war in Syria, but wanted to leave Turkey because he feared for his life.
He was threatened by male gangs carrying knives, who said they wanted to rape him. One friend, who identified the body, told the organisation it was so mutilated, he was only recognisable from his clothes.
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Homosexuality has been legal in Turkey since 1923, when the republic was founded. It was also legal in the Ottoman empire from the mid-19th century.
However, gay people in Turkey regularly complain of harassment and abuse in a largely conservative Muslim society, where same-sex relationships are frowned upon.
Authorities in Istanbul banned the annual gay pride march in June for the second year in a row, citing security and public order fears.
The incident has provoked horror, with Willy Fautré, director of the Brussels-based NGO, Human Rights Without Frontiers, telling this website, "While gay people are victims of hate crimes in Turkish refugee camps, the EU turns a blind eye and a deaf ear to their desperate calls for help for the sake of good relations with President Recep Tayyip Erdoğan."
Fautré added, "What's the use of EU specific guidelines for the protection of vulnerable groups such as gay people, if the EU deports such refugees to Turkey without any effective protection?
"When some categories of refugees are at risk of being sent back in a hostile environment, the EU should prioritise their security and grant them asylum."
The tragedy has put the EU/Turkey asylum deal under the spotlight once again.
Under the EU-Turkey deal reached in March, Ankara agreed to take back Syrian migrants arriving in Greece in exchange for billions of euros in aid and visa-free European travel for Turkish citizens.
But relations between Ankara and the West have deteriorated over criticism against Turkey's President Recep Tayyip Erdoğan's massive crackdown following last month's failed coup.
On Tuesday, Erdoğan accused the EU of not having disbursed the financial aid it had promised, or delivering visa liberalisation for Turkish citizens traveling to Europe.
European Commission President Jean-Claude Juncker recently admitted that the EU-Turkey refugee deal could collapse.
"The risk is great. The success of the pact so far is fragile. President Erdoğan has several times hinted he wants to terminate the agreement," he said.
A Commission spokesperson for migration, home affairs and citizenship said that the EU remained committed to the deal but added that the challenge was greater than that agreement alone.
In September 2015, EU leaders committed to relocate 160,000 people from Italy and Greece by September 2017. In total, just 3056 people have been relocated (2213 from Greece and 843 from Italy).
Greece's migration minister, meanwhile, has warned that a "Plan B" is needed in case the EU-Turkey refugee deal collapses amid escalating tensions between the bloc and Ankara.
In an interview with the German daily Bild, Yannis Mouzalas said, "We are very worried. We need a Plan B."