Musiala first went down during Saturday's friendly against RB Leipzig before a further episode struck on Tuesday against Heidenheim, only minutes after coming off the bench.
The 23-year-old later confirmed on social media that he has been diagnosed with "brief, temporary but easily treatable episodes of absence" linked to a neurological dysfunction, adding that doctors have found no further health risk and that he intends to continue playing.
"There I was speechless, which is rare enough," Hoeness told RTL of the second incident. "It's a drama, especially for Jamal. The fact that it happened again four days later really knocked me for six."
The timing has hit Hoeneß particularly hard, given the club's hopes for the player heading into the new season.
"We always believed a new era for Jamal would begin after the World Cup," he said. The Germany international can count on the club's full backing, Hoeness added: "With these two incidents on Saturday and yesterday, it's obviously a problem, first and foremost for the person Jamal. I go to bed with him on my mind in the evening and wake up thinking of him in the morning."
Bayern Munich say they have since received written confirmation from specialists that there are no concerns over Musiala continuing to compete in elite-level sport, though independent medical experts have cautioned that more information would be needed to determine the specific cause of his episodes.
Musiala signed a contract extension with Bayern until 2030 last year and remains one of the club's most important attacking players heading into the new campaign.
Hoeness said the club had been aware of the underlying issue for some time, though this was the first occasion it had manifested visibly during matches.
Musiala's own statement struck a reassuring tone, telling supporters he is "doing well" and thanking them for their concern while asking to be given space to manage the situation alongside his medical team.