The former Juventus midfielder experienced a recent row with the Real fans following the club’s poor form, but Capello stated that Emerson’s fitness is the reason behind his exclusion.
"Emerson isn't in the side because I spoke to him after training and he told me the shin splints he suffers from were painful," Capello told a news conference on Saturday.
"He said he didn't want to play with (painkilling) injections because we have two important games coming up when we'll need every player available. I don't see it as him being afraid to play in the Bernabeu."
Real Madrid will have a crucial week as their last 16 Champions League second leg clash with Bayern Munich on Tuesday will be followed by the Spanish derby against Barcelona over the weekend.