Hazard watched from the stands as his team-mates beat Real Valladolid 1-0 at the Estadio Alfredo Di Stefano on Wednesday.
"He's a bit affected and sad," Courtois said afterwards when asked about Hazard.
"He was training very well this week and was looking forward to returning.
"He had his usual pace back.
"This new injury is a small setback, but it's not his ankle."
During Wednesday's game, Courtois made a number of crucial stops to keep Real Madrid's clean sheet intact.
"We knew it would be a tough game," the goalkeeper said.
"They managed to draw with us at home last season.
"In the first half they weren't dangerous, but I had to make three good saves in the second."