The former Porto man has refuted suggestions that he tried to injure the Argentine attacker and claims he was only trying to do his best for his team on Wednesday evening
The Portugal international's performance has caused controversy after the former Porto man was spotted standing on the hand of the Ballon d'Or winner.
However, the 28-year-old centre-back has confirmed through Madrid's official website that there was no malice intended in the incident.
"With regard to the play involving Leo Messi, it was an involuntary act. But even still, if Messi is offended, I apologise as I was only intending on defending my team," Pepe said.
"I give myself body and soul [in games] and it never goes through my head to hurt a colleague."
The two men will come face-to-face again when they meet at Camp Nou next Wednesday for the second leg of the tie.