The Italian news agency ANSA quoted Pantani's manager, Manuela Ronchi, as saying the cyclist was out riding his bike when the verdict came in. In Italy, defendants can choose not to attend trial.
Ronchi quoted Pantani as saying: "They tell me today that this trial shouldn't even have started."
The sports fraud charges stemmed from an incident during the 1995 Milan-Turin race, when Pantani's red-blood cell count tested at almost 60 percent above normal during the race.
A high red blood cell count can indicate the use of EPO, a growth hormone considered the drug of choice in endurance sports like cycling. It can also occur naturally.
Pantani, the 1998 winner of the Tour de France, has denied any wrongdoing.
Pantani crashed during the race and had to be hospitalized. Defense lawyers argued that his red-blood cell surge was due to dehydration.
In December a court in Forli convicted Pantani of the charges. Besides the suspended sentence, he was also ordered to pay a 1.2 million lire ($552) fine.
Cycling federation President Gian Carlo Ceruti expressed satisfaction at Tuesday's acquittal, saying the decision was "good on the personal level and also good for the sport."
Italian cycling has seen some ugly times recently. In this year's Giro d'Italia, the nation's most prestigious cycling race, police raided the hotel rooms and vehicles of all teams in a search for evidence of doping. Under Italian law, taking or administering banned substances in sports is punishable by up to three years in jail.
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