Various Spanish news organisations speculated Carvajal had bitten Mandzukic on the elbow and then punched the Atletico Madrid striker in the abdominal region, citing blurry footage from the Vicente Calderon.
Mandzukic was involved in a number of scuffles against Real, with the Croatian forward also suffering a cut to his face after an elbow from Sergio Ramos.
But Carvajal argued he did nothing wrong.
"I saw after the game that I am accused of biting an opponent player," the 23-year-old wrote on Twitter.
"Let me make clear that I have not bitten anyone, nor attempted to do so."
Atletico coach Diego Simeone was asked at his media conference about the alleged incident between Carvajal and Mandzukic - "I didn't see it" was his response.
The 44-year-old Argentine added that he thought Ramos' elbow on Mandzukic was accidental.
