The Ghana international was left out of Schalke's 0-0 draw against Steaua Bucharest in the UEFA Champions League on Tuesday due to a knee injury.
Boateng offered to play in Romania, but coach Jens Keller said his decision to rest the 26-year-old was the right one ahead of the meeting with Stuttgart.
"Kevin-Prince Boateng doesn't really need breaks. He offered playing on Tuesday even though his knee hurt, but based on the overall situation I decided not to let him play," Keller said.
"We play Tuesday and Saturday and if he sacrifices himself now it wouldn't help us in the future.
"The international games didn't go that well for him, he couldn't receive treatment but I decided to not bring him on Tuesday. Now he's without pain so it wasn't a bad decision."
Schalke midfielder Julian Draxler is also expected to be fit in a huge boost to Keller's side, who sit sixth in the Bundesliga.
Keller is wary of a Stuttgart team who have struggled this campaign and will want to respond after a 2-0 home loss to Borussia Monchengladbach last time out.
"Stuttgart have a great team, they also have got some good new players, but at the moment things aren't going the way they want them to," he said.
"Of course they are looking to be higher in the league after their transfers in the summer, but every match in the Bundesliga is a difficult one, and they certainly won't be an easy opponent here.
"Stuttgart want to respond after their loss at home last week. We must have that in mind. Also we had a match earlier this week - they haven't.
"But we want to have these busy weeks and now we're looking forward to this match at home in front of our amazing crowd."
