Hans-Wilhelm Muller-Wohlfahrt announced his decision to step down on Thursday due to a break in the "bond of trust", having claimed his medical team were made responsible for Bayern's 3-1 UEFA Champions League quarter-final first-leg loss to Porto on Wednesday.
Muller-Wohlfahrt, who also serves as doctor for the Germany national team, previously stepped down in 2008 when Jurgen Klinsmann was coach, but returned after the ex-Germany international departed.
Asked about his future following Muller-Wohlfahrt's exit ahead of Saturday's Bundesliga game with Hoffenheim, Guardiola said: "Of course I will be staying here next season."
Guardiola was also quizzed on footage that appears to show him sarcastically clapping in Muller-Wohlfahrt's direction after Medhi Benatia picked up a hamstring injury at Bayer Leverkusen last week.
"It was my disappointment. Nothing to do with the doctor," Guardiola added. "Benatia has struggled with injuries for a long time and that's why I was frustrated. We need him."
Turning his attention to the progress of Bayern's high-profile absentees, Guardiola said: "[Philipp] Lahm won't play tomorrow. He's sick. [Franck] Ribery is also not fit.
"[Bastian] Schweinsteiger won't be in the squad, but it's looking better. These players are my heroes.
"Over the last few weeks and months, despite injuries, they've played every minute and are still here.
"We are strong with the team that we have, this is a strong fighting group."
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