The former Germany international also lashed out at the Catalan coach for rotating his squad too much and constantly switching Philipp Lahm between defence and midfieldReal Madrid was the result of Pep Guardiola's misguided attempt to get Bayern Munich to play like Barcelona.
The Catalan coach spent four years in charge of the Blaugrana between 2008 and 2012, during which time he revolutionised the game with a possession-orientated style of play which became known as 'tiki-taka'.
Matthaus, though, says Guardiola has made an error in trying to get Bayern to embrace a footballing philosophy that is alien to many of his squad, citing the 4-0 Champions League loss at home to Madrid as a painful case in point.
"You cannot get them to play Catalan here," the former Bayern ace told AC. "You cannot expect Bayern as Barca plays."
Matthaus also attacked Guardiola's decision to begin rotating players after Bayern had clinched the Bundesliga title at the end of March, arguing that the constant chopping and changing between domestic and European fixtures affected the Bavarians' "rhythm".
"There were too many changes," the ex-Germany international stated.
"The ship may not have begun to go off course had it not been for such dramatic rotation."
In addition, Matthaus queried Guardiola's propensity for constantly moving captain Philipp Lahm between full-back and midfield, arguing that it "contributed to the uncertainty in the team; to a historic result [a 5-0 aggregate] to Madrid, a debacle."
However, Matthaus felt that Guardiola had also been let down by his players, feeling that they had not taken sufficient responsibility for their Champions League capitulation.
"They were not self-critical enough," he fumed. "If Bayern now lose to Borussia Dortmund in the DFB Pokal final, there will be serious talks on Sabener Strasse [Bayern's headquarters]."