The Team Type 1-Sanofi rider, 27, won the opener on Tuesday but slipped out of contention after finishing back in 11th on Wednesday.
He rallied in style though, beating French duo Armido Fonseca (Bretagne Schuller) and Julien Simon (Saur Sojasun) on the line after a 189.1km ride from Jumilhac-le-Grand to Trelissac.
The previous leader, Lithuania’s stage two winner Evaldas Siskevicius, had been part of a seven-man break, but that was reeled in with 80km left by Simon’s Saur Sosajun team.
The general classification is topped by Kocjan, with Simon second and La Pomme Marseille’s Siskevicius third.
- Julien Simon
- Saur Sojasun