Dutchman Afellay has been nursing a muscle injury for weeks as Schalke have slipped down to seventh in the league, triggering the sacking of former coach Huub Stevens on Sunday a day after their 3-1 home defeat to Freiburg.
Keller was named as the new coach until the end of the season.
"Afellay will not be at our disposal tomorrow," Keller said, adding he was satisfied with the team's first training session under his guidance.
"The team listened to me and executed well what I wanted them to do. It is the mental aspect that is important tomorrow. I have to remind my players of their strengths."
Schalke, through to the Champions League round of 16, turned their domestic season on its head when they failed to win any of their last six games and lost four of them to drop from second to seventh after a superb start.
Keller said he had little time to implement anything new for the game on Tuesday.
"That game will not be so much about my philosophy or how I want to see the game played," said Keller, whose previous Bundesliga experience was a brief spell at Stuttgart in 2010.
"We have to be strong tomorrow and courageous and let's hope the fans will give us their full support."