Sections of the media have reported that the center back grabbed the Portugal international by the throat and punched him in the face inside the club's treatment facilities after Sunday's game, but Ballesteros has dismissed those wild allegations.
"I've never assaulted anyone in my life, especially not Pepe," he told reporters.
"After 20 years in this profession you can believe anything I say. I went in to see how Cristiano [Ronaldo] was, that is all. I would never dare to assault anyone.
The Granotes player was also disappointed with comments made by Sergio Ramos. who suggested he should swap football for boxing in light of the allegations.
"That's what hurt me the most. Before the game I congratulated him and [Iker] Casillas for what they had achieved with the national team and what he said surprised me," he added.
"These things happen because it involves Madrid, it is not a coincidence."