Guardiola's arrival two years ago was supposed to herald another great European era for the Bavarians after their 2013 treble. They had reached the Champions League final in 2010, 2012 and 2013 before signing him.
The 44-year-old has so far failed to take the side beyond the semi-final stage in his two seasons in charge, Tuesday's 3-2 win not enough to give them a place in next month's final.
And while Bayern won the domestic double last season and the league this time around it was to capture a sixth elite European trophy that he was brought to the club.
Bayern's ambitious bosses wanted European glory and they wanted it fast, and who better to bring it than the most sought after football coach in the world?
Guardiola has received the full backing of the Bayern board from the very start.
He was even described as an exceptional coach after they lost to Leverkusen in the league, crashed out of the German Cup, went down 3-0 to Barcelona and were beaten by Augsburg in the league last week to round off their first four-game losing streak since 1991.
Guardiola won 14 titles in four seasons at Barcelona, including two Champions Leagues, but Bayern's 5-3 loss on aggregate to the Spaniards has proved to everyone in Munich that he is no magician.
"We won the league, now we will rest, we will go on holidays and come back next season stronger," Guardiola said. "I am not bothered about how critics view my work. I am not there for them. I am there for the club."
Critics may not be an issue for him but with one year left on his contract and no talks yet on an extension Guardiola will need to review his options.
The squad is in need of a revamp with several of the players who carried the team to the three finals in four seasons now in the twilight of their careers.
Bastian Schweinsteiger, Franck Ribery, Arjen Robben and captain Philipp Lahm are all 30 or older, with Xabi Alonso, who joined this season, also in the 30-something age group.
A Bayern rejuvenation is unlikely to be completed in just one season.
Whether Guardiola stays on to oversee the project beyond 2016 or chooses to leave, one thing is certain -- his grace period in Munich ended on Tuesday.
(Reporting by Karolos Grohmann)
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