The Croatia international was left out of the squad for the victory over Borussia Monchengladbach last Friday, prompting speculation over his future, particularly with Robert Lewandowski set to join the club in the summer.
Guardiola says that the striker remains a valued part of his team, but cannot be offered any guarantees as to whether he will feature from the start.
"I will wait until after the final training session and decide afterwards," he told reporters. "We have a big squad, one or two players won't be included in the squad every week.
"He's a great player, but that's the case with all of our players, otherwise they wouldn't be here. You know my decision, my opinion. Something I need these players, sometimes others. I need to make a decision."
Meanwhile, Bayern CEO Karl-Heinz Rummenigge has insisted that Mandzukic's relationship remains as strong as ever after 18 successful months in Bavaria.
"We had a good discussion with Mario's agent. Our relationship is basically good. And don't forget that Mandzukic had a big impact in 2013," he said. "Guardiola said Mandzu will be back if he trains well."
Bayern Munich and Stuttgart face off at the Mercedes Benz Arena on Wednesday.