Barrionuevo and his security chief Rafael Vera were each sentenced to 10 years in prison for their part in the "dirty war" of the mid 1980s, allegedly organised by the Socialist government of Felipe Gonzalez, against the Basque separatist group, Eta.
They - and 10 other defendants - are accused of having ordered and paid for the kidnapping of a Basque businessman, Segundo Marey, who was mistaken for an Eta hitman.
Last week leaks to two national newspapers said the court had decided to hand down 13 year sentences.
This was denied by the court, and there was speculation that the sentences would be changed because of the leaks.
Political repercussions
Barrionuevo is first former government minister to go to jail since democracy was restored to Spain in the 1970s.
Many more trials are expected over the "dirty war" scandal - which the BBC Madrid correspondent Frank Smith says was the main reason the Socialist Party lost the last election two years ago after almost 15 years in government.
He adds that repercussions arising from the guilty verdicts could end the political career of Barrionuevo's immediate boss at the time of the kidnapping - the former Prime Minister Felipe Gonzalez.
'No mitigating circumstances'
Former Civil Governor Julian Sancristobal, was also sentenced to 10 years after two weeks deliberating by a panel of 11 judges. Seven agreed the men were guilty.
Supreme Court Justice Joaquin Delgado sentenced Barrionuevo, Vera and Sancristobal on two counts: misappropriation of public funds and the Marey kidnapping.
He said there were "no mitigating circumstances" for the offences.
The three men were also given 12 years of absolute disqualification which prevents them from holding any public honours, jobs and posts they may have, even if they are elected.
Anti-Basque death squads
The trial probed the connection between the former Socialist government and a shadowy armed gang called the Anti-Terrorist Liberation Groups, or Gal, comprising members of the security forces and hired assassins.
Gal is held responsible for murdering 28 people they suspected of being Eta members between 1983 and 1987.
It was later discovered that at least a third of them had no connection to the armed group.
Eta has accused the government of being behind Gal's operations, but Mr Gonzalez has always denied any knowledge of the death squads.
Socialist Party reacts
The Socialist Party said they believe Barrionuevo and Vera are innocent.
Party spokesman Alfredo Perez Rubalcaba said: "There are four judges who have registered private votes defending the innocence of Jose Barrionuevo.
"I want to tell you that this is exactly our position.
"We share the views of these four Supreme Court judges, who disagreed with the sentence and in their personal verdicts are saying that Jose Barrionuevo and Rafael Vera are innocent."
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