Rafael, 22, joined United with his brother in the summer of 2008 and has made 52 Premier League appearances in four years.
He suffered extensively from injury problems last season when being restricted to only 10 league starts but is very much a part of United's future, according to Sir Alex Ferguson.
“Rafael is one of the club’s brightest young prospects; he has no fear of playing and has great belief in himself," Ferguson told the club's official website.
"The boy has developed immensely since joining United, his energy and enthusiasm are a joy to watch. Rafael has all the attributes to become one of the best full-backs in the world and I am delighted he has signed a new contract.”
Rafael added: “I am so happy to sign a new contract. I love playing for Manchester United; there is a great team spirit here and a real desire to win.
"My time here has been unbelievable; winning two league titles, a league cup and a Club World Cup has made me hungry for more trophies. I would like to thank Sir Alex for his belief in me and I would also like to thank the fans for their support.”
Fabio has made only 21 appearances for United, with injuries also hampering his development, and he will now spend the coming season with QPR.
"I'm so happy to be here," Fabio said. "This loan is so important for me in terms of my career. I want to play as many games as possible here. I want to play well and win games as well.
"It's a good move for my career and for my confidence. Sir Alex Ferguson said that I'd enjoy it here and told me to play as many games as I can.
"I know that QPR is a Club with great history. I read about the history and that's why I'm here. I also came here because I'm ambitious. I want to help QPR progress up the Premier League. Hopefully the fans will enjoy watching me in action, because I'll do my best."
Meanwhile, United have formally confirmed the departures of Tomasz Kuszczak, Michael Owen, Liam Jacob and Joe Coll on free transfers.