In an official statement on the Manchester United website last night entitled "Player websites warning" the club said all official news relating to the club would appear on its official website ManUtd.com.
"The club wishes to make it clear that no Manchester United players maintain personal profiles on social networking websites. Fans encountering any web pages purporting to be written by United players should treat them with extreme scepticism.
Any official news relating to Manchester United or its players will be communicated via ManUtd.com," the club said in its statement.
Along with Twitter accounts for Rooney and Giggs, Darren Fletcher's Twitter account has also been removed.
Some reports have said that the Facebook accounts of Giggs, Wes Brown and Rio Ferdinand have had their content removed, but this morning the official pages of those are still up and running on the social networking site despite the apparent ban.
Social networking sites and Twitter in particular pose major problems for football clubs trying to closely manage their communications as stars use them as a direct avenue to talk to the fans and more importantly the press.
Earlier this week Liverpool player Ryan Babel complained on Twitter about a planned swap that would send him to Sunderland, igniting the ire of manager Rafa Benitez.
Babel, In a series of tweets, wrote: "The boss left me out the squad. No explanation. I never had a fight with the manager. I always kept quiet.
"Where did it go wrong? You have people who support me and don't support me and one day, you will see what I'm capable of.
"Will it be at LFC or somewhere else - I have faith."
Last summer Tottenham Hotspur striker Darren Bent risked possible action after he attacked the Premier League club via his Twitter account as he was in the process of leaving the club - also for Sunderland.
Over several posts he wrote: "Do I wanna go to Hull City NO Do I wanna go Stoke NO do I wanna go Sunderland YES so stop fucking around Levy.
"Seriously pissed off now" and "Why can't anything be simple. It's so frustrating hanging around doing jack shit".
In the US many sports stars use Twitter across the NFL, NHL, MBA and MLS, creating controversy. Last year New York Yankee Nick Swisher was accused of having his tweets sent by his publicist.
San Francisco Giants pitcher Brian Wilson removed his account after posting apparently drunken tweets and Antonio Cromartie, star player for the San Diego Chargers, was fined $2,500 (£1,400) by the NFL for commenting about the team's nutrition on Twitter, saying that "nasty food" was to blame for the Chargers' poor performance last year.