The 18-year-old has impressed at right-back this season and has been rewarded with a new deal that will keep him at Old Trafford until June 2013.
“Everyone at the club has been very impressed and excited by his first year as a professional,” United boss Sir Alex Ferguson told the club’s official website.
“His enthusiasm and the adventurous way he plays is typical of a Manchester United player and we are delighted that he has signed a new contract.”
Rafael added: “It has been a fantastic first year and I have been learning from all the players at the club but especially from the defence.
“It has been an exciting time for me and I want to be part of this for a long time so to get an extension is unbelievable.”