Rooney's kick at Montenegro's Miodrag Dzudovoic last Friday was judged "an assault" by UEFA's control and disciplinary panel, who stuck to the letter of the law in handing out the punishment despite a plea for leniency from the Football Association.
It means Capello now has to judge whether to take Rooney as part of his squad to Poland and Ukraine, and hope that he can make an impact if England make it through to the quarter-finals.
The question on all of England's mind: Who will replace Rooney?
The FA will wait for the full reasons behind the decision before deciding whether to appeal. The ban could even be increased by an appeal panel, but that would be unlikely and it looks odds on that the FA will try to have the suspension reduced.
The Manchester United striker is understood to be extremely disappointed in the outcome but will follow the FA's advice about any appeal.
Former England striker Alan Shearer described the ban as "a huge blow" to England's chances in the European Championships, and called the kick "a silly error".
Shearer told BBC Radio 5 Live: "It's a huge blow. It's not only a huge blow to the team, to the fans and to football followers but to Wayne himself because he realises he's made a stupid error.
"I still think whoever replaces him in the team, England still should have enough to get through the three games without him."
Phil Neville, Rooney's former team-mate for United and England, labelled the ruling "a joke".
The Everton midfielder said on Twitter: "Rooney banned for 3 games what a joke- if it was a Dutch Spanish Italian german player they wouldn't even get 1 game #fact."
Rooney was shown a straight red by German referee Wolfgang Stark for kicking Dzudovoic - England boss Capello admitted it was a "silly mistake" by the 25-year-old, who immediately put himself in danger of receiving the three-match ban.
UEFA's disciplinary regulations state that a player will receive a "suspension for three competition matches or for a specified period for assaulting another player or other person present at the match".
A UEFA statement said: "Today's decision was taken in relation to the red card shown to Rooney for assault after 74 minutes of England's final Group G game, the 2-2 draw with Montenegro in Podgorica.
"The striker will now be suspended from playing in his country's next three UEFA national competition matches for which he would be eligible."
The FA have three days to decide whether to appeal, and they said in a statement: "Further to UEFA's decision to impose a three-match suspension on Wayne Rooney following his sending-off against Montenegro, the FA await the full reasons from the disciplinary committee, and will give full consideration to the decision internally, before deciding on any response to UEFA or making any further public comment."
The FA had taken some hope from a previous case involving Andrey Arshavin, who was given a two-match ban and missed Russia's first two games of Euro 2008 after being sent off against Andorra. But in that case television evidence was less clear cut than in Rooney's.
In 2004, Chelsea's Marcel Desailly was initially handed a three-match ban for elbowing Monaco's Fernando Morientes but that was reduced on appeal to two games after UEFA said the act was not deliberate.