Scholes came out of retirement in January and produced a number of impressive displays as United were just beaten to the Barclays Premier League title by neighbours Manchester City.
The new deal for Scholes was first announced by United manager Sir Alex Ferguson, and Wednesday's announcement confirms that formalities have now been competed.
In a statement on their official website, United also confirmed goalkeeper Ben Amos has agreed a three-year contract extension.
Confirmation of Scholes' deal comes almost a year to the day since he announced his retirement.
The 37-year-old moved into a role with United's coaching team but after reversing his decision to retire he made his comeback in United's FA Cup third-round derby victory over City at the Etihad Stadium on January 8.
He went on to make 16 Premier League appearances in the second half of the season, scoring four goals, giving rise to speculation he could end his international exile and force his way into Roy Hodgson's squad for Euro 2012.
That Scholes did not return to the international fold will come as a relief to Ferguson, who in announcing the new deal earlier this month admitted that next season would likely be the midfielder's last.
"I am delighted," Ferguson told MUTV on May 14. "He knew he had made a mistake. He now realises if he plays 25 or 30 games next season, they will be of real quality.
"I think this will be Paul's last season. We know him very well. We have had him since he was a kid. We know how to use him."
Source: PA
Source: PA