Musiala has not featured for Bayern since collapsing on the pitch in successive pre-season friendlies against RB Leipzig and Heidenheim last month.
The 23-year-old later confirmed on Instagram that he had been diagnosed with absence seizures caused by a neurological dysfunction, adding that there was no additional health risk and that he intended to continue playing as before.
Bayern Munich have said the episodes were triggered by a change to medication he had been taking for the condition, which the club has been aware of since last season.
Speaking to ARD on Tuesday evening, Eberl explained the club's approach to bringing the midfielder back into contention.
"With Jamal, the situation is that after the last two incidents we're trying to build up a period without seizures," Eberl said.
"I believe it can go away completely — that's the big hope — but that's difficult. First this seizure-free period, and once that's there, he can be back out on the pitch with us."
Bayern face Schalke away on Saturday in their second Bundesliga fixture of the season, and head coach Vincent Kompany was cautious when asked whether Musiala might be involved.
"Maybe. But I don't want to put any more pressure on the boy," Kompany said on Sky. "He's doing well, he's doing better. If things continue like this, it won't be much longer."
Kompany confirmed Musiala is fit and has resumed full training with the squad.
Elsewhere, Eberl also addressed the ongoing contract talks with Harry Kane, who scored twice in Bayern's DFB-Pokal win over VfL Osnabrück to continue his prolific record in front of goal.
The 32-year-old's current deal expires at the end of the season, with the length of any extension proving the main sticking point — Bayern want to tie him down until 2029, while Kane is said to prefer a deal running to 2030.
"It's relative to call it a formality," Eberl said. "The talks have to happen, just as the games have to be played, that's clear. What can be said is that both sides want it, and then it should work out. Whether it'll be easy, I don't know, but we remain confident."