The new deal will keep the 23-year-old at United until the summer of 2016.
United boss Sir Alex Ferguson told the club’s official website: “The last player I remember making an impact as big and as quickly as Javier is Ole Gunnar Solskjaer and he reminds me of Ole a lot.
“His talent for creating space in the box and his finishing ability mark him out as a natural goalscorer. Off the pitch, he is a pleasure to manage. He works very hard and is a popular member of the squad.”
Hernandez joined United from Chivas de Guadalajara in July 2010 and made an immediate impact at Old Trafford.
“Playing for Manchester United has been a dream come true for me,” insisted Hernandez. “I never expected my first year to go so well and I’m delighted to commit my future to United.
“To win a title and appear in a Champions League final was fantastic. I’m looking forward to helping my teammates as we bid to win more trophies for this great club.”