The centre-back was forced off 16 minutes into the Audi Cup final defeat at the Allianz Arena while Bale did not feature, having played in the win over Tottenham a day earlier.
With Madrid's La Liga opener against Sporting Gijon just over two weeks away, Benitez played down any fears over the pair's fitness.
"Pepe already had a niggle and to avoid an injury we brought him off," he explained.
On Bale, Benitez continued: "Playing two games in two days - we didn't want to risk him.
"It wasn't advisable to play the players who played yesterday. We put Danilo on to have a bit more pace on the right but the main thing is the players and the aim is to keep working, while protecting the squad.
"The great thing about the players up front is that they can swap positions and each one knows what they have to do.
"I think it was positive for the experience of the young players and the work we did as a team, but I'm sad about the defeat.
"They had an extra gear over us and it showed. We lacked a little bit of possession and didn't have the ball high up the pitch enough to be able to create danger.
"And without that, the team little by little moved backwards. We had a few counters, but not enough to win."
