The Blues goalkeeper was involved in a collision with Gary Cahill and Stoke striker Peter Crouch during the 4-0 win over the Potters at the weekend.
Courtois, who had a successful two-year loan with Atleti, will be fit to go up against his former club though after Conte confirmed it is nothing serious.
"I spoke with our doctor about Thibaut, above all about whether I could make a different substitution and he said Thibaut was okay and you can make another substitution," Conte said after seeing his side thrash Stoke.
"Now he is okay and ready to play the next game against Atletico Madrid."
Chelsea do not have any other fresh injury problems going into the game, but Conte is likely to tinker with the side that put Stoke to the sword in convincing fashion on Saturday.