Rooney signalled to the bench that he wanted to come off the field with around two minutes left of the game that England had already wrapped up.
But Capello made the United star stay on the field as he had used up all of his substitutions.
But after the game came the report that Rooney was suffering from a minor neck problem.
"He said he had a small problem in his neck but it is not a problem," said Capello.
"He wanted to come off for the last two minutes but I had made all the substitutions so it was impossible to change.
"Rooney is okay. At this moment he just needs to play and find his form."