Later, the 36-year-old rider was sacked by his team BMC.
Ballan was punished by CONI's anti-doping tribunal after it ruled he had contravened article 2.2 of the World Anti-Doping Agency (WADA) code relating to "the use or attempted use of banned substances".
A statement from CONI confirmed the "responsibility of the athlete Alessandro Ballan in contravening article 2.2 of the World Anti-Doping Code and imposes a suspension of two years with effect from January 17, 2014 until January 16, 2016.
Ballan was suspected of being embroiled in a doping affair which has also implicated two doctors, Guido Nigrelli and Fiorenzo Egeo Bonazzi -- both of whom were alleged to have aided his attempt to procure and use banned substances.
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CONI prosecutors had initially requested the ban on the basis of evidence supplied by a public prosecutor in Mantua.
CONI banned Nigrelli for life and Bonazzi for four years.
The statement punished Nigrelli under "article 2.7 and 2.8 of the World Ant-Doping code and has ordered him to be banned from practising for life from January 17, 2014.
Ballan had previously been suspended by BMC due to allegations of doping but after being cleared by the Swiss-American team the Italian, a former winner of the Tour of Flanders, resumed racing again in May 2010.
BMC have said in recent days they were standing by Ballan pending the outcome of the tribunal.
However in keeping with the team's strict anti-doping policy, Ballan's contract was terminated later on Friday.
BMC, speaking through president/general manager Jim Ochowicz, said in a statement: "The BMC Racing Team announced Friday that it is terminating the contract of Alessandro Ballan.