The 29-year-old had surgery on the condition, which affects both his feet, last June but found himself still struggling to run after seven months of rehabilitation and has now called time on his career.
The prop admitted he was disappointed he could not finish his career on the paddock but claimed he had done everything possible to get back to full fitness.
"I persevered and fought hard, and I gave it a lot of thought but, in the end, I've been left with no alternative," said Scott.
"(But) being an inaugural member of the Force is something that will stay with me forever.
"I will miss the mateship and camaraderie. But all of us have to face up to life after rugby at some stage, and my time is now."
Scott made his Super rugby debut in 2000 playing for the Brumbies where he won 12 Super caps before moving to the Reds for the 2004 season for nine appearances.
He joined the Western Force in 2005 and picked up 16 Super caps with the Perth-based team, bringing his final tally to 37.
Force coach John Mitchell reflected that Scott was a fine prop who could play both sides of the scrum.
"Gus was one of the best loosehead props in Australia," he said. "It's just a shame he couldn't have had one more season, but there's no controlling these things.
"We'll certainly miss his non-stop chatter."
However, Mitchell acknowledged Scott's retirement would present an opportunity for homegrown RugbyWA Academy prop, Kieran Longbottom, to step up into the role.