The Spaniard appeared to trample on the head of the centre-back in the latter stages of the first period at the Bernabeu, but Busquets has quelled such claims.
"Nothing happened with Pepe," the 25-year-old told reporters.
"I didn't touch him. It's nonsense. If I stamped on his head he'd have a size-45 mark or stud marks. It's something pushed by the press. But we live in a country where they can show this lack of respect. Let everyone say what they want."
Barcelona are in Champions League quarter-final action against Atletico Madrid on Tuesday.