Pepe denied intentionally treading on Messi in the 2-1 defeat and the incident, caught on television cameras, was apparently missed by the referee, who had earlier booked the Portuguese for a late tackle on Sergio Busquets.
The 28-year-old Pepe, who was left out of Sunday's La Liga win at home to Athletic Bilbao, is available for the game at the Nou Camp after the Spanish football federation (RFEF) decided on Monday to take no action against him.
At a news conference where his often difficult relationship with the media hit a new low, a tetchy Mourinho said Pepe and midfielders Lassana Diarra and Esteban Granero had minor injuries and a decision on their availability would be taken on Wednesday.
"There are three players with problems, including Lass and Granero," Mourinho, who gave curt responses to most of the questions he was asked, told reporters.
"If he is physically fit he'll play," he said of his compatriot Pepe.
Barca decided not to report Pepe over the incident and said it was up to the football authorities to take the initiative.
President Sandro Rosell, responding to the federation's decision to stand pat, said Spain could learn from countries like England.
The English FA on Monday charged Manchester City striker Mario Balotelli with violent conduct following an incident in Sunday's Premier League match against Tottenham Hotspur when he appeared to stamp on the head of Spurs midfielder Scott Parker.
The referee took no action but Italian Balotelli was subject to a so-called retrospective action and could be banned for four matches.
"It would be good if with Pepe one took the example of what happens in countries like England," Rosell said.
"When someone jumps a red light the police should punish them even if the pedestrian who gets run over does not report it."
INACCURATE MOLES
The Pepe incident has added extra spice to the cup second leg but Mourinho batted away several questions about what tactics he plans to employ to try to reverse Real's woeful run of results against their arch rivals.
Last week's defeat at the Bernabeu was Mourinho's fifth against Barca in nine games since he joined Real and he has only managed one win in a 'Clasico', a 1-0 success after extra-time in last year's cup final.
"I won't answer," he said when probed about his plans. "I am the coach and the decision is mine and I don't have to announce it publically."
Asked about an unsourced report in the Spanish media that he plans to leave Real in June, the former Chelsea and Inter Milan manager added: "Did I say that? Ask your colleague."
Another reporter asked him if he was happy at Real and Mourinho answered with a vague murmur that appeared to indicate he was.
Responding to an enquiry about why he thought some Real fans had whistled him in Sunday's win over Bilbao, he said curtly: "I don't know. You'll hav
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