Ibrahim al-Hussein, 27, carried the torch through Eleonas camp, where some 1,600 asylum seekers are being given temporary shelter amid Europe's worst migrant crisis since World War II.
Dressed in the official Rio 2016 white shirt with yellow sleeves, Al-Hussein lit his torch from that of Greek Olympic Committee president Spyros Kapralos amid a joyous crowd of refugees at the camp in an industrial suburb of Athens.
"It is an honour for me. It's great not just for me but for all the refugees," said Hussein.
Hussein, who has been granted asylum by Greece, was nominated for the Olympic torch relay by the Greek Council for Refugees, the UN refugee agency's local implementation partner, a UNHCR source told AFP.
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"From the start the aim was to have a refugee who has secured asylum," the UNHCR source said.
"We had asked if there is a refugee who is also a star athlete," the source added.
Hussein, an electrician from Syria's Deir Ezzor province on the Iraqi border, was a successful swimmer and judoka before war erupted.
The family lived on the banks of the Euphrates River, and Hussein told UNHCR that the Deir Ezzor suspension bridge would often serve as his diving board.
"I used to climb to the top, dive into the water and swim in the river," he told the UN refugee agency in an interview published on its website.
But in 2012, he lost half of his right leg in a bombing and fled for Turkey a year later. From there, he travelled to the Greek island of Samos in 2014 on an inflatable boat.
With the gift of a prosthetic leg from a private doctor, Hussein now works in a cafe in Athens, lives in a rented apartment and continues to be a passionate sportsman.