The midfielder stated that the angry response that followed his exit from Wednesday’s game against Stuttgart was down to shock
With Bayern trailing 1-0, Kroos was replaced on the hour mark by Mario Mandzukic, before goals from Claudio Pizarro and Thiago gave the league leaders a 2-1 victory.
Kroos threw off his gloves and ignored his team-mates on the bench when leaving the pitch for Mandzukic and then revealed exactly why he had responded in that manner in a post-match interview.
Talking to Bild, Kroos said: "I simply did not expect to be substituted. Of course I have to accept that. Plus, I was really angry we were behind."
The Germany international’s contract expires in June 2015 and reports have linked the 24-year-old with a move to Manchester United after talks stalled over a new deal.
But Bayern CEO Karl-Heinz Rummenigge has claimed that the club want to keep Kroos and will work on a suitable deal.
"I hope we will reach an agreement with Toni. He is a player that we want to keep in general,” said Rummenigge.
“Now we have to see whether we will manage to get a contract that satisfies Toni and FC Bayern the same way."