Le Clos was admitted to hospital in Durban to have four wisdom teeth removed, two weeks ahead of the global showpiece.
Taking a cautious approach, his management team had held off before booking his flights to Doha on Tuesday, after ensuring there were no complications.
“He’ll be going to the world champs. He is sore but feeling a lot better than yesterday,” his father, Bert le Clos, confirmed.
“He’s taking a few days off training, but I’m sure he’ll get some in before he leaves.”
The 22-year-old Olympic and world champion will spearhead the South African team at the five-day biennial short-course spectacle, held in a 25m pool, starting on December 3.