The Spaniard has made it clear that the midfielder's lack of game time of late is related to neither his contract dispute nor his reaction to being substituted against Stuttgart.
The Germany international was an unused substitute in this month's wins over Eintracht Frankfurt and Nurnberg, with speculation rife that his demotion was a result of his public display of displeasure at being replaced in the match against Stuttgart on Jan. 29.
However, Guardiola has made it clear that neither Kroos' reaction against Stuttgart nor his refusal to sign a contract renewal played a part in his thinking.
"Kroos was benched for tactical reasons," the former Barcelona boss said at a press conference. "It is not the first time that a player is unhappy with one of my decisions. A player is always unhappy when he doesn't play. It's up to me to keep the situation under control.
"Toni Kroos has already done a lot for Bayern, not just for me, but for the entire team."
Kroos could be reinstated to the starting XI for Wednesday's DFB-Pokal game against Hamburg.
The 24-year-old has a contract with the Bundesliga club until June 2015 and Manchester United is reportedly monitoring his situation at the Allianz Arena with interest.