Ibrahim al-Hussein, who has been given asylum in Greece, bore the torch through Eleonas camp.
The 27-year-old electrician used to swim and do judo competitively in Syria.
He is among more than one million migrants to have entered the EU, crossing to Greece by inflatable boat.
Mr al-Hussein now has a prosthetic leg, works in an Athens cafe and plays wheelchair basketball.
He can swim 50m (yards) in 28 seconds, three seconds off his personal best before the injury, and will compete in the Greek disabled swimming championship in June.
He told AFP news agency it was an honour to carry the flame.
"I am carrying the flame for myself but also for Syrians, for refugees everywhere, for Greece, for sports, for my swimming and basketball teams," he said.
"My goal is to never give up. But to go on, to always go forward. And that I can achieve through sports."
Meanwhile, the International Olympic Committee (IOC) has said a team of up to 10 refugees will take part at the Rio Olympics.
A selection process is due to take place in June, AFP quoted a UNHCR official as saying.
The Olympic flame was lit last week in the 2,600-year-old Temple of Hera at Ancient Olympia.
On Wednesday it will be handed over to Brazilian officials in a ceremony at the historic Olympic stadium in Athens, site of the first modern Games in 1896.
Some 12,000 torchbearers will then carry the flame through Brazil before the Games start in August.
A Syrian refugee who was a sportsman before losing part of his leg in a bombing has carried the Olympic flame through an Athens refugee camp.