Former Germany striker claims that the Chilean broke a promise to his side when he confirmed his move to Italy, but the 59-year-old was nonetheless sympathetic to the player
Earlier on Thursday, the 24-year-old confirmed his transfer to the Turin side.
Neither club have declared the move official, but a statement is expected to be released in the near future.
"[Vidal] has broken his word," Hoeness told Bild in response to the player's statement.
The former forward was nonetheless sympathetic to the Chile international, who would have faced a difficult situation had he waited another season to move to Munich.
"It would have taken great backbone to play at Bayer Leverkusen, having made the statement: 'I am going to Bayern'. And I would not expect the player to have such backbone," he said, according to Spox.
Vidal revealed his desire to join the Allianz Arena outfit in mid-June, but after Leverkusen insisted they would not sell him to a rival Bundesliga club, the player was left in a stand-off with his employers.
A previous Bild report claimed that Vidal had promised Bayern coach Jupp Heynckes by phone that he would only move to Munich, be it before the end of the current transfer window, or when his contract expires next summer.
"He will not go to Juventus. And also not Lazio or elsewhere. Arturo Vidal will come to Bayern. If not this summer, then the next," Heynckes said following the alleged phone call.
But Juventus tabled a sufficient offer to both club and player, and appear to have landed the versatile midfielder.
Even though his coach was taken by surprise, Hoeness insisted that he never considered Vidal's signing a probable scenario.
"I always thought that with that kind of transfer, the odds were below 50 per cent," he said.
"I thought to myself: if it works, it's nice; if not, it's OK."
The latest word from Munich is that Bayern will not seek an alternative to Vidal.