Around 10 hours after he first went to Manchester to finalize the deal on transfer deadline day United finally announced a deal worth 27 million pounds (US$48.3million) to Everton.
But Rooney needed two visits to Manchester hospital for checks on how his broken foot was healing. Rooney suffered a broken metatarsal bone in his right foot playing against Portugal at Euro 2004 in June and is out of action for at least another month.
United announced the move around 7 p.m. (1800 GMT) after it had passed on the details to the Stock Exchange.
"Manchester United is delighted to announce that it has finalized an agreement with Everton Football Club for the transfer of Wayne Rooney the club said in a statement.
"Wayne has signed a six year contract until 30 June 2010."
"The fee payable to Everton is 20 million pounds (US$36 million). Half is due now with half due on 1 August 2005. In addition there are contingent payments to Everton over the next five years up to a maximum of 7 million pounds (US12.6 million) dependent on club success the player renewing his contract and his appearances at international level."
The move which had been pending for nearly two weeks was sealed with time running out on transfer deadline day.
Everton announced during the morning that the 18-year-old England striker went to United's Carrington training complex after earlier tests at a Manchester hospital.
United then issued a statement to the Stock Exchange suggested that the agreement was dependent on the player's fitness.
"Manchester United plc has reached an outline agreement with Everton FC for the transfer of the registration of Wayne Rooney subject to his successful completion of a medical the statement said.
"Details of the agreement will be announced when all terms are complete."
Rooney was photographed alongside a smiling United manager Alex Ferguson walking alongside the Old Trafford pitch. But he later left the stadium and returned to hospital for further checks on the broken foot which will keep him out of action for another month.
Despite the problems over the injury United clearly felt it was worth spending a major fee on a talented striker who could bring back the league title and even Champions League success.
United is already seven points behind big title rivals Arsenal and Chelsea in the championship race having won just one of its first four games.
Rooney was one the biggest stars of Euro 2004 with four goals until he suffered his injury against host Portugal in the quarterfinal. England lost the game in a penalty shootout.
When Rooney completes the move he will be competing with Dutch star Ruud van Nistelrooy Frenchman Louis Saha and England's Alan Smith for a place on the United strikeforce.
Van Nistelrooy has not played so far because of a knee injury and United has made a poor start to the campaign. Ferguson's team coincidentally held 0-0 by Everton at Old Trafford on Monday has won just five points from four games and is seven behind defending champion Arsenal and Chelsea who have each gained a maximum 12.
Everton had hoped to keep a young striker who made his league debut at age 16 for the Toffees and scored a memorable matchwinning goal against Arsenal two seasons ago.
But Newcastle and Manchester United each made bids to lure the young striker away from Goodison Park and Rooney angered the Everton fans by making a written transfer request saying he wanted to play for a team in the Champions League.
Rooney who has already made 17 appearances for England was already a rising star when made some standout performances at Euro 2004 scoring twice in each of two victories over Croatia and Switzerland.