The UCI said in a statement that the Saxo-Tinkoff rider had been stripped of his results from the Japan Cup that month but would face no further sanction.
Rogers, a three-times trial world champion and team captain at last year's Tour de France, had been provisionally suspended in December.
The UCI said it had analysed Rogers' explanations and accompanying technical reports and found "a significant probability" that contaminated meat was to blame.
Rogers had raced in China before travelling to Japan.
"As a result, the UCI has proceeded with the automatic disqualification of Mr Rogers' results at the 2013 Japan Cup Cycle Road Race but, after consulting WADA, decided that he should not be sanctioned any further."
The World Anti-Doping Agency has for some years warned athletes about the dangers of meat in China and Mexico containing the banned anabolic steroid.
Rogers' Spanish team mate Alberto Contador was handed a two-year ban after a positive test for clenbuterol on the 2010 Tour de France. He argued he was the victim of food contamination.
The UCI said it was monitoring the latest developments carefully and would continue to take steps to ensure riders were properly informed.
It repeated, however, that the presence of clenbuterol in a urine sample constituted an anti-doping rule violation under the World Anti-Doping Code and its own rules.
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