The 27-year-old took his tally to seven goals in his past six games after netting twice against the Clarets in Sunday's Premier League clash at St Mary's, which finished 3-1 to the Saints.
Asked if Austin's impressive form made him a shoo-in for Thursday's Europa League clash at San Siro, the Frenchman said: "No, it's important he doesn't play all the games from the start.
"It's important you don't lose Charlie, it's important he's available every time, to keep a good physical level for every player.
"Charlie is not an endurance player - it's important to keep him with his qualities, and we can change the team every game. It's not possible, for me, for a player to start all the games every three days."