The 26-year-old Manchester United striker was originally banned for three matches following his sending off for kicking opponent Miodrag Dzudovic in their final qualifier against Montenegro in October.
"The three-match suspension levelled against Wayne Rooney is now suspended, with the third game of the suspension, suspended for four years, so Wayne will be available for the final group game of the European Championships against Ukraine," Adrian Bevington, the managing director of Club England, told reporters at UEFA's headquarters.
"It is effectively a two-game suspension with one carried over for a four-year period for the national team."
He added: "I am pleased to say we have had a very fair hearing from UEFA's panel and we are very pleased with what's happened today."
Both Rooney and England manager Fabio Capello gave evidence to the hearing.
Rooney will now miss England's opening two Group D matches against France in Donetsk on June 11 and Sweden in Kiev on June 15, but will be eligible to play against co-hosts Ukraine in their third and final group game in Donetsk on June 19.
The sanction applies to national team competition governed by UEFA so the suspended third-game ban would only come into effect if he is sent off for violent conduct in a European Championships match, the FA said.
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