The 21-year-old joined La Liga side Valencia on a season-long loan during the summer transfer window, but his long-term future remains at Old Trafford having agreed to extend his stay.
Pereira, who has made 13 appearances for the United first team, has put pen to paper on a deal which will keep him at the club until 2019, with the option of a further year on top of that.
"I am delighted that I have extended my contract with this great club. The manager is building a great team here and I want to be part of that as soon as possible," he told the club's official website.
"I am going to continue my development at Valencia this season in the hope that I will get plenty of minutes on the pitch. I would like to thank the manager for his help and guidance and for the faith he has shown in me."
Manager Jose Mourinho added: "Andreas is already a very good footballer. He is a young player with great natural ability and a good attitude towards continuing his development. I have no doubt that he has the potential to be one of the future great players of this club."
Pereira, who has been with United since the age of 16, spent last season on loan with Granada, where he scored five goals in 35 league appearances.