The Croatia forward was omitted from Bayern squad's for the 2-0 win at Borussia Monchengladbach last Friday, leading to further reports that he is set to leave the club.
Guardiola was reportedly unimpressed with Mandzukic's performances in training following the announcement that Robert Lewandowski will join the German and European champions at the end of the season.
Juventus and Manchester United are just two of a host of clubs who have been linked with a move for the 27-year-old, who has scored 10 goals for the Bavarian giants this term.
Bayern coach Guardiola has not decided if Mandzukic will be back in the squad to face Stuttgart on Wednesday, but played down talk of a rift with the former Wolfsburg man.
He said at a press conference on Tuesday: "After a workout, I'll decide (whether Mandzukic will feature against Stuttgart),
"We have a big squad. In every game I have to decide for 18 players. It will happen almost every week, that one, two, three super-super players can not in the squad with us."
Guardiola became increasingly irked by questions about Mandzukic and stressed that the decision to leave the striker out against Gladbach was for the good of the team.
He added: "This is the third question about Mandzu. That's enough. You know my opinion. There is no problem. It was my decision for the final game.
"In the first round Mandzu played. For Thomas Muller or Claudio Pizarro sometimes not. In this situation, I see and analyse what is best for the team. That's the only reason. There is no other."
Wingers Franck Ribery and Arjen Robben will play no part against Stuttgart due to "muscular problems", while Holger Badstuber, Bastian Schweinsteiger, Daniel van Buyten and Javi Martinez all remain sidelined.
Robben came on as a substitute in Friday's win at Gladbach following a spell on the sidelines with a knee problem, but revealed after the game that he is still not fully fit.
