Real defeated Manchester City 4-3 in the shootout.
Neuer, 38, suffered an adductor injury two weeks ago.
Guardiola said that to be part of the titles, they need everyone.
The footballer died of a heart attack.
Musiala suffered a muscle injury earlier this month and has been sidelined since.
Bayern Munich managed to clinch a hard-fought victory against Galatasaray, handing the Turkish team their first defeat of the season.
United have several injury issues to deal with and have confirmed Sergio Reguilon will be absent against Crystal Palace on Saturday.
Jonny Evans, who was making his first United start after eight and half years, provided Fernandez with the assist for the goal from the middle of the pitch.
The UEFA Champions League group stage draw for the 2023/2024 season is out.
England international forward Harry Kane has completed a move from Tottenham to Bayern Munich on a long-term permanent deal.
