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The honourary Bayern president, a former player and coach of Germany's most successful club, was quoted as saying in Monday's edition of Bild newspaper that Barca would "try everything to throw Bayern off balance".
"They will deploy all methods, anything that's allowed and anything that's forbidden. They will defend themselves because their pride has been hurt," he added, according to Bild.
Barca, mistakenly referring to the German daily as "Blind", published a statement from Beckenbauer later on Monday in which he apologised if he had been "misunderstood".
"I only said that Barca will do what it can to get to the final, but not by illegal means," he said.
"When I say they will use everything they have at their disposal I'm referring to putting pressure on their rival, something that's normal on the pitch, it's something that I used to do as a player and during my time as a manager.
"Barca are one of the biggest and most honest clubs in the world and they have all my admiration.
"I'm convinced that 'fair play' will preside over the match on Wednesday. The two teams will do everything possible to get to the final, and that's what I meant to say."
Bayern, leading 1-0 at half-time, played a flawless second half against Barca - widely considered the best team of the past five years - to notch up another three goals and take a huge advantage into the second leg at the Nou Camp.
"Barca will try to take Bayern's eyes off their game plan with one-on-one duels. The Bayern players should not be drawn into personal battles," the 67-year-old Beckenbauer, who won three consecutive European Cups with Bayern in the 1970s, told Bild.
"They will not surrender, they will provoke, they will try all the tricks in the book," the paper quoted him as saying.
Bayern, who have already won the Bundesliga and are in the German Cup final, are bidding for an unprecedented treble of titles for a German club.
The Bavarians are also aiming for their third Champions League final in four seasons after losing the 2010 and 2012 finals to Inter Milan and Real Madrid respectively.
