Ronaldo started the first leg last week, which Madrid won 1-0, despite a period on the sidelines through injury, but Bale was only named on the bench due to illness.
Ronaldo also started Madrid's 4-0 win over Osasuna in La Liga at the weekend, but Bale was not involved as the Welshman battles to overcome a flu-like virus.
"In the end it doesn't matter who plays, the individual quality of the Madrid players is amazing," Guardiola told reporters at a press conference.
"They are all direct runners. That said, I'm sure they'll play Bale and Cristiano because they are very important to them."
Bayern are the current holders of the Champions League.