"I have a clear conscience," Scarponi said. "I accept the verdict of three months, even if I hoped it would have been possible to avoid sanction."
Lampre rider Scarponi's ban started on October 1, meaning that the Italian will be allowed to resume competition at the start of the 2013 season.
Ferrari, who has denied any wrongdoing, was banned for life by the US Anti-Doping Agency which said he had masterminded Lance Armstrong's doping programme during the years the American dominated the Tour de France.
All contact with Ferrari has been outlawed by the Italian cycling federation since 2002.
Scarponi admitted for the first time that he had visited Ferrari on October 25 after the Italian sports daily La Gazzetta dello Sport published a report containing extracts from a Padua investigation into the doctor.
The 33-year-old has already served an 18-month ban for his involvement in the Operation Puerto blood doping scandal.