The English champions have endured a tough season as they currently sit seventh in the Premier League and were eliminated from the Champions League by the Bavarians on Wednesday.
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"I think that Sir Alex Ferguson got on the right train and left at the right time," he told Sky when asked what he thought of Moyes' side's performance.
Reflecting on the match, Beckenbauer believes that Guardiola's decision to withdraw Mario Gotze in favour of Rafinha proved decisive as Bayern came from behind to charge into the semi-finals.
"The substitution of Gotze was decisive," he added. "Gotze couldn't prevail against the robust defence and it was entirely logical that he was taken out.
"Guardiola then made changes so the midfield was better organised, with Philipp Lahm in central midfield."
Thomas Muller put Bayern ahead after Mario Mandzukic had cancelled out Patrice Evra's shock opener and Beckenbauer feels the Germany forward has the same instinct as his namesake Gerd.
"Gerd Muller was defined by scoring goals in such situations and in this case, Thomas copied that," he added.
"They have been together often enough and shot TV commercials together. The goal was the logical consequence [of them spending time together]."