The Portuguese admitted to being very aggressive with referee Chris Foy at the end of the game at Loftus Road and launched a tirad at the official who had awarded both a penalty to the home side, and sent-off two of his players.
However, Villas-Boas has decided to contest the charge.
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."
After Foy awarded Rangers an early penalty for David Luiz's foul on Heidar Helguson, which saw the Icelander give the hosts the lead, both Jose Bosingwa and Didier Drogba were dismissed.
Following the indisciplined afternoon, which saw seven Chelsea players booked, the club were fined £20,000 after admitting to a charge of not being able to control their players.
Following the game 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 OK 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.
"A couple of decisions are right, yellow cards for sure, but I think he [Foy] lost it before and was card happy towards the team. I'm not happy with the difference of treatment. I don't think the same treatment was applied.
"Apart from the fourth official, the other three were led by the emotions of the crowd and couldn't deal with a game like this. Three of the games played by Chelsea were influenced by the referee, and this is not Premier League level.
"You have to trust human error, but it's a big pattern for us. Things are not going our way. Conspiracy theories can lead to bans and lead to you calling us crybabies, and we're not. But it keeps happening.
"We're showing commitment and strength. Hopefully, things will go our way, referee decisions going our way."
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