"I want to categorically deny that I made any kind of racist insult towards any Sevilla player," the Spanish international and former Arsenal captain wrote on his Twitter account after local media reported the accusation.
"I will not tolerate anyone accusing me of things that I'm not," added the 24-year-old.
"If they are frustrated by a decision that has gone against them on the football pitch then there are others ways to deal with it.
"To cry racism is cowardly and an easy option to excuse your own poor behaviour. My conscience is completely clear. I've done nothing wrong."
While he did not mention Fabregas by name, Kanoute said earlier on Sunday he had been "provoked and insulted" during a mass brawl which erupted after Barca were awarded a penalty in second-half stoppage time.
Before the kick was taken, an angry Kanoute kicked the ball away from the spot and then appeared to grab Fabregas around the throat before being sent off. Lionel Messi's effort was then saved by goalkeeper Javi Varas.
Kanoute wrote on his Twitter account that he regretted the incident -- which came at the end of UEFA's Football Against Racism in Europe (FARE) week -- saying it "was not a good example".
"Nonetheless there was provocation and insult, as you are already aware," the former Tottenham Hotspur player said, without referring to Fabregas by name.
"But don't think about it anymore. His behaviour, like mine, was bad. Issue closed. Let's get on with the football."
Fabregas said he had "always maintained the best relationships with my team mates who came from different backgrounds, races, religions and nationalities."
"No one has ever accused me of being racist or bigoted in all my years of playing in the game," he said.
"There is a simple explanation for that. I have never behaved in that manner. "I share a dressing room with a Malian player (Seydou Keita), I have an Arab tattoo and my partner is Lebanese. There is no better indication that it makes no sense."
Fabregas's Barca team mate Daniel Alves defended the Spaniard at a news conference earlier on Sunday.
"There are moments when your pulse is racing and you don't say please when you are asking for things," the Brazlian defender said.
"But it's clear there was no racist insult, above all from Cesc, who is a fantastic lad and would never do that."