The Portuguese admitted after the game he had been "very aggressive" with referee Chris Foy after accosting him post-match at Loftus Road, and accused the official who sent off two of his players in the Barclays Premier League game of failing to treat the teams equally.
But, after he was handed an FA charge for improper conduct earlier this week, Villas-Boas on Monday denied the allegation. A statement from the Blues read: "With regards to the FA charge against Andre Villas-Boas for remarks he made after the QPR game, the manager is denying the charge against him and has submitted his response to the Football Association."
The 34-year-old has been less than impressed by some decisions against his team, even calling referees' chief Mike Riley to complain about the performance of the officials in a defeat at Manchester United, while he was also critical of decisions in their draw at Stoke.
Speaking after the defeat at QPR, Villas-Boas said: "The ref was poor, very very poor. And it reflected in the result.
"I spoke to him at the end and I was very aggressive to him. I don't care if he's okay or not.
"Everyone can have a bad day, but this was not a bad day for us. It was a good day for us and a bad day for the referee."
QPR won the game 1-0 thanks to a Heidar Helguson penalty which was awarded for a needless David Luiz challenge in the eighth minute.
Foy then controversially sent off Jose Bosingwa after deeming he was last man when bringing down Shaun Wright-Phillips, and was left with no choice but to dismiss striker Didier Drogba for a two-footed lunge.
The referee booked seven more Chelsea players, with the club being fined #20,000 after admitting to a charge of failing to ensure their players conducted themselves in an orderly fashion.
Source: PA
Source: PA