The surprise announcement by the hard-line judiciary confirmed one of the opposition's most devastating and embarrassing claims against authorities and the elite Revolutionary Guard forces that led the crackdown after June's disputed presidential vote.
There was no immediate public reaction from the opposition, but some activists asserted that authorities under pressure over abuse claims were merely seeking to punish low ranking staff while shielding senior level officials who the opposition says are most to blame.
Still, the statement offered some rare vindication for the government's critics, who had rejected earlier explanations from the police and the judiciary that the detainees' deaths were caused by illnesses like meningitis, not physical mistreatment.
"The coroner's office has rejected that meningitis was the cause of the deaths and has confirmed the existence of signs of repeated beatings on the bodies and has declared that the wounds inflicted were the cause of the deaths," the judiciary statement said, according to the Web site of Iran's state TV.
The judiciary also said it has charged 12 officials at Kahrizak prison - three of them with murder, but it did not identify them. The prison, on the southern outskirts of the capital, Tehran, was at the center of the opposition's claims that prisoners were tortured and raped in custody.
Anger over the abuse claims, which emerged in August, extended far beyond the reformist camp, with influential conservative figures in the clerical hierarchy condemning the mistreatment of detainees.
The outrage forced Supreme Leader Ayatollah Ali Khamenei to order the immediate closure of the Kahrizak facility.
The opposition says at least 72 protesters were killed in the postelection crackdown, but the government puts the number of confirmed dead at 30.
Authorities initially tried to repel the abuse claims by accusing the opposition of running a campaign of lies against the ruling system. President Mahmoud Ahmadinejad had even accused Iran's enemies of being involved in the crimes, a claim the opposition rejected as ridiculous.
Iran's police chief, Gen. Ismail Ahmadi Moghaddam, said in August that protesters were beaten by their jailers at Kahrizak, but he maintained at the time that the deaths were not caused by the abuse.
The opposition's criticism was implicitly aimed at the country's most powerful military force, the Revolutionary Guard, which operates with some autonomy from the ruling clerics and led the harsh crackdown and detention of protesters in the tense weeks after the election.
The unrest broke out after pro-reform candidate Mir Hossein Mousavi claimed he was robbed of the presidency through massive fraud in the vote.
Pressure around the abuse claims accelerated in early August.
One of the other pro-reform candidates defeated in the election, Mahdi Karroubi, said then that he had received reports from former military commanders and other senior officials that some detainees, male and female, were raped in custody to the point of physical and mental injury.
It also emerged that one of the detainees who had died in custody was the son of Abdolhossein Rouhalamini, a top aide to conservative presidential candidate Mohsen Rezaei. That was a central factor in raising anger among government supporters.
His son, Mohsen Rouhalamini, was arrested during a July 9 protest and taken two weeks later to a hospital where he died within hours.
Saturday's judiciary announcement named him as one of the three people it had found to be victims of abuse. The other two were identified as Amir Javadi and Mohammad Kamrani.
Further adding to the outcry, prosecutors said this month that a doctor who exposed the torture of jailed protesters died of poisoning from a delivery salad laced with an overdose of blood pressure medication.
Their findings fueled opposition suspicions that he was killed because of what he knew.
The 26-year-old doctor, Ramin Pourandarjani, had testified to a parliamentary committee, reportedly telling them that one of the protesters he treated was the younger Rouhalamini and that he died from severe torture. He said he was also forced by security officials to list the cause of death as meningitis, according to opposition Web sites.
Pourandarjani died on Nov. 10 in mysterious circumstances, and authorities initially gave conflicting explanations, saying he was in a car accident, had a heart attack or committed suicide. Forensic tests later showed that the doctor died of "poisoning by drugs" that matched doses of propranolol found in a salad that was delivered to him, Tehran prosecutor Abbas Jafari Dolatabadi said early this month.
The government's rivals did not immediately respond directly to the judiciary's statement Saturday.
One prominent reformist voice, former President Mohammad Khatami, told an audience of academics in western Iran on Saturday that the use of force against protesters demonstrates the government has little regard for human rights.
"A majority of the people are dissatisfied with the way the country is being administered," his Web site quoted him as saying.
He added that "a considerable portion of society" has objections over the official election results.
"These must be heard. They (people) must be convinced that the elections were really fair. Such convincing can't be achieved through jail, crackdowns and restrictions," Khatami said.
Iran's judiciary has also had a central role in authorities' efforts to silence the opposition. Since August, it has brought to trial more than 100 protesters, activists and pro-reform opposition leaders, accusing them of fueling the protests and being part of a plot to overthrow the government.