The 23-year-old, who is currently out of action with a fractured thumb, has agreed terms that will keep him with the county until December 2016.
Yorkshire director of cricket Martyn Moxon has said that he is delighted to secure Root's future.
"I'm looking forward to seeing Joe continue his progression as a Yorkshire and England cricketer," Moxon told BBC Sport.
"His desire to be the best that he can is a perfect example to our young players that if you work hard on your skills and have total commitment, you can achieve almost anything in your profession."
Root has played 34 first-class matches for Yorkshire.