The Bayern Munich coach will make do without the services of the striker against Borussia Dortmund on Saturday, allegedly for a disciplinary issue
The Croatian has played a key role for the Bavarians this season, scoring 26 goals in all competitions for the German champions.
However, he has clashed with the Catalan before - when he was excluded from the team in January - and has been dropped ahead of the Olympiastadion clash, allegedly over a disciplinary issue.
"He would have been able to play. But it is my decision and that's it," the Spaniard told reporters.
Additionally, Bastian Schweinsteiger has been ruled out as he is still nursing knee problems.
The coach said: "He was not able to train this week. Schweinsteiger is injured. I hope he can travel to the World Cup in Brazil. But I am no doctor."
Guardiola went on to say that he is eager to cap his first season in the Bundesliga with further success, having already won the European Super Cup, the Club World Cup and the Bundesliga.
"I'm very proud of what we've achieved so far this season. We're ready to take on Dortmund. I'm really looking forward to this final."
Bayern and Dortmund kick off in Berlin at 20:00CET on Saturday.