Rooney, who will also miss the home Premier League match against Fulham on Saturday, has been punished for his four-letter rant into a live camera during United's 4-2 league win at West Ham United last weekend.
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"I am gutted to miss two matches, I am not the first player to have sworn on TV and I won't be the last," Rooney said on the Man United website.
"Unlike others who have been caught swearing on camera, I apologised immediately. And yet I am the only person banned for swearing. That doesn't seem right."
Rooney ran to the camera after completing his hat-trick from the penalty spot with his obscenities clearly heard by millions of viewers worldwide.
While United accepted the charge against Rooney of using abusive language they felt the suspension was excessive and appealed.
In a statement the FA said: ""Rooney had admitted a charge for the use of offensive, insulting and/or abusive language, but claimed that the automatic penalty of two games was clearly excessive.
"The commission did not accept the claim and Rooney will begin the standard two-match suspension with immediate effect."
He added to Saturday's hat-trick when he scored the only goal in United's 1-0 win over Chelsea at Stamford Bridge in the first leg of their Champions League quarter-final on Wednesday.
The England striker is free to play in the return leg next Tuesday as that game is under UEFA's control and not the FA's.
"Manchester United is clearly very disappointed with the Regulatory Commission's decision," the club added.
"Wayne Rooney apologised immediately after the match and the club now wishes to move to on to what hopefully will be a very exciting conclusion to the season."
