The Roten president accused the team of "playing like rubbish" after it scraped through to the quarterfinals, while former keeper Oliver Kahn delivered a similarly damning verdict in his column for Bild.
Beckenbauer feels that criticism can often inspire a team to reach greater heights, citing his own harsh words following a 3-0 loss to Olympique Lyonnais in 2001, when Bayern eventually won the Champions League.
"Uli Hoeness has done everything right. He had to act as responsible. That was just as necessary as my speech in Lyon," he told Bild.
"Even young players will respond when criticized publicly. Bayern played at a lower class in the second leg than they did in the first. Next time Matthias Sammer can strike again ..."
Bayern clashes with Juventus in the last eight of the competition.