Pepe appeared to stamp on the hand of Messi while the Argentinian forward was on the ground during Barca's 2-1 win in Madrid, prompting widespread criticism, and Mourinho warned the Portugal defender he would face disciplinary action if it was seen to be deliberate.
But Mourinho has now accepted Pepe's claim the contact was accidental, and will include him in the squad to play Athletic Bilbao if he can shake off a hamstring problem sustained during the match.
"Pepe is on the squad list, but we have yet to see if he'll be fit enough to play or not," Mourinho said. "I have to call up other players for his position. If he can't make it someone else will. They're all good.
"Pepe apologised and that's enough for me. I'd only be angry if Pepe publicly said what he did was not intentional after admitting privately that it was. Those who think he's a liar should say so and assume the consequences.
"It's your right to call him a liar if you wish to, but you must assume the consequences. It would be an issue between you and the person you accuse of lying."