Pepe picked up a leg injury during Real's 1-0 loss against Bayern. In fact, he had to leave that game. Now, the Portuguese defender will have to miss Real's debut against Sporting Gijón, although the club did not confirm how long he will be out.
It seems reasonable to give Pepe more time to recover properly from this injury, so Varane will be the one replacing him.
Real Madrid will also be without Karim Benzema for that first match. Injuries are usual during the pre-season, but Benitez will not be happy about losing two of his potential starters weeks before the official start of the season. Madrid are surely hoping to have better luck with their injuries this season after players like James and Modric missed a big part of the 2014/2015 season, hurting Real's chances of winning titles.
Pepe should be available for Real's first home game against Betis, just like Benzema.