That would mean Briton Chris Froome, who finished second ahead of Bradley Wiggins in the race, could be awarded the victory for his seventh Grand Tour crown.
"The anti-doping tribunal found (Cobo) guilty of an anti-doping rule violation based on abnormalities from 2009 and 2011 detected in his biological passport and imposed a three-year period of ineligibility on the rider," UCI said in a statement.
"In accordance with the procedural rules of the anti-doping tribunal, the decision will be published on the UCI website in due course."
A biological passport is an electronic record where results of all doping tests by a rider over a period of time are collated and compared.
The UCI said that Cobo had used a prohibited substance but did not state what it was.
Cobo can appeal the decision before the Court of Arbitration for Sport within a month.
Froome is currently in intensive care in France following surgery after a crash at the Criterium du Dauphine on Wednesday that ruled him out of next month's Tour de France.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Toby Davis)
