The Lotto-Belisol rider led home Matteo Pelucchi (IAM Cycling) and Maxime Daniel (Sojasun) at the conclusion of the 146.5km stage between Limoux and Gruissan.
Schleck was forced to abandon the race on the first day "due to an infection of the respiratory tract", according to his Radioshack-Leopard Trek team.
"This morning I already had breathing problems," said the rider. "Instead of getting better, it just got worse during the race because of the cold and the wind.
"I didn’t want to abandon out of respect for the fans and the organisation, but also because I need this competition. After the Tour Down Under I felt I was in a good way and I was really looking forward to this race.
"I am now sicker than I was before. I need to let my body recover and I hope I can resume training as soon as possible. In theory my race programme will not change."
The team added that he will likely return at the Tour du Haut-Var on February 16-17.