State comptroller Manuel Galindo imposed a “sanction of disqualification from exercising public office for a period of 15 years,” his institution said in a ruling made public by Capriles himself on Friday.
Capriles said on Twitter that he rejected the move and insisted he would retain his post as governor.
The move effectively bans Capriles from running against socialist President Nicolas Maduro in a general election due next year.
If effective, it will remove from the political ring one of the most prominent contenders in the centre-right opposition that is pushing to remove Maduro from office.
Capriles branded the move part of what the opposition alleges is a “coup” by Maduro, who is resisting opposition calls for a vote on removing him from power.
“This is all part and package of the internal coup,” Capriles said on Twitter.
Capriles lost narrowly in the 2013 election that brought Maduro to the presidency after the death of Maduro’s mentor Hugo Chavez.
Venezuela’s political crisis intensified last week when the Supreme Court issued rulings curbing the powers of the opposition-controlled legislature.
The rulings by the court, which has consistently ruled in Maduro’s favour during the crisis, drew international criticism of Maduro’s camp.
The court revoked the moves days later, but the opposition maintained its claim that Maduro’s side was attempting an institutional “coup d’etat.”
Capriles can appeal against his sanction within two weeks to the comptroller and within six months to the Supreme Court.
The collapse in prices for Venezuela’s crucial oil exports has sapped the country’s revenues, prompting shortages of food, medicine and basic goods along with a surge in violent crime.
The opposition blames Maduro for the economic crisis. He says it is due to a capitalist conspiracy.
Violence erupted for a third straight day on Thursday at protests against Maduro, leaving one demonstrator dead.
The wave of protests has revived fears of broader unrest in Venezuela, where 43 people were killed during riots in 2014.
The country has undergone three attempted military coups since 1992.
Pregnant Venezuelans pour into Colombia for medical attention