The Chelsea manager admitted he was "very aggressive" with Foy after accosting him post-match at Loftus Road, and accused the official who sent off two of his players of failing to treat the teams equally.
A statement from the Football Association confirmed: "Chelsea manager Andre Villas-Boas has been charged with improper conduct by the FA, following media comments he made about the match official after his side's match at Queens Park Rangers on 23 October 2011.
"Villas-Boas has until 4pm on 15 November 2011 to respond to the charge."
The 34 year-old is in his first season at the Stamford Bridge helm after replacing Carlo Ancelotti over the summer.
The former Porto manager has been less than impressed by some decisions against his team, even going so far as calling referees' chief Mike Riley to complain about the performance of the officials in Chelsea's Premier League defeat at Manchester United. 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 sent off Jose Bosingwa for a last-man challenge 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 west London club being fined £20,000 after admitting to a charge of failing to ensure their players conducted themselves in an orderly fashion.
Villas-Boas continued in his post-match rant: "A couple of decisions are right, yellow cards for sure, but I think he 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."
The Chelsea manager added: "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 cry babies, 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."