An 80 million pound fee for the player was agreed between the clubs last month and United reported on its Web site on Wednesday that the fee has now been paid.
United manager Alex Ferguson paid tribute to the Portugal winger.
"Cristiano has been a marvelous player for Manchester United. His six years at Old Trafford have seen him develop into the best footballer in the world," Ferguson said. "His contribution has been a major factor in the club's success in that time and his talent, his ability to entertain and his infectious personality have enthralled fans the world over."
"Everyone here wishes him well in his future career," Ferguson added.
Meanwhile, Lyon has denied Spanish media reports that Real Madrid had signed its striker Karim Benzema, saying that while it had received a bid for the player, Madrid was not necessarily the bidder and no deal had yet been concluded.
"We have received an offer markedly higher than the figure mentioned, but nothing proves that it has come from Real Madrid," Lyon's director of communications Olivier Blanc told the Web site of sports daily L'Equipe on Wednesday. "There is no deal in place with anybody."
Spanish media reported that Madrid had signed Benzema for 35 million euros, but the Spanish club did not comment on the reports.
Meanwhile, David Villa appeared closer to signing with Barcelona following a reported meeting with the team's sporting director Txiki Begiristain.
The striker ate with Begiristain on Wednesday according to newspaper El Comercio.
Chelsea and Manchester United are also vying for the 27-year-old striker's services, with Real Madrid pulling out of the running last week after balking at Valencia's reported asking fee of 50 million euros.