Both players were unable to train on Friday when they nursed injuries ahead of Real's final friendly fixture against Fiorentina in Warsaw on Saturday, a game they were treating as a key warm-up for their reunion with Atletico.
Coach Carlo Ancelotti, rotating his squad before meeting Atletico again for the first time since they beat them 4-1 in the all-Spanish Champions League final in Lisbon in May, made nine changes to the team that started Tuesday's UEFA Super Cup final against Sevilla in Cardiff, which Madrid won 2-0.
Only Cristiano Ronaldo, who scored both goals, and newly-arrived playmaker James Rodriguez were retained as Madrid, the King's Cup winners, finalised their preparations. Ronaldo scored an early goal but Real lost 2-1 to Fiore.
Bale trained on his own while Pepe did only some light stretching. Both, however, were on the bench in Warsaw. French defender Raphael Varane is likely to replace Pepe while Spanish midfielder Isco is tipped to step in for Bale, if he is unfit for the clash at the Santiago Bernabeu.
Ronaldo issued a warning to Atletico and all their rivals after Real's win in Cardiff that the European champions are aiming for a clean sweep of all six trophies available to them including the Spanish Super Cup and their local rivals' La Liga crown. "We are going to try to win all the trophies," he said. "It's good to win this trophy (the European Super Cup) to give confidence to the team and let's see next week against Atletico what we are going to do."
Boosted by the combined $160.76 million arrival of three World Cup stand-out players in Rodriguez, Germany midfielder Toni Kroos and Costa Rica goalkeeper Keylor Navas from Levante, they hope to retain the King's Cup and the Champions League. Ronaldo acknowledged that they will face determined, if much-changed, opponents in Atletico on Tuesday.
Since their disappointment in Lisbon on May 24, Atletico have sold Spain striker Diego Costa and Brazilian left back Filipe Luis to Chelsea, who have also recalled Belgium goalkeeper Thibaut Courtois from his loan at the Calderon. They have also lost important squad players including former Spain striker David Villa.
In their place, coach Diego Simeone has spent about 95 million euros to sign highly-rated forwards Mexican Raul Jimenez and Frenchman Antoine Griezmann, from America and Real Sociedad respectively, and Slovenian goalkeeper Jan Oblak from Benfica to compete with Miguel Angel Moya from Getafe. He also signed Croatia striker Mario Mandzukic from Bayern Munich, among others.