The two other victims were identified as Amir Javadi and Mohammad Kamrani.
A report on the Iranian judiciary's website said the military court had also sentenced nine other suspects in the case to flogging or prison terms, while one person was acquitted.
No details were released on the identities of the suspects or when the verdict was handed down.
Authorities initially denied the abuse claims, accusing the opposition of running a campaign of lies against the ruling system.
But in August, influential figures in the clerical hierarchy condemned the mistreatment of detainees.
The outrage forced Ayatollah Ali Khamenei, Iran's supreme leader, to order the immediate closure of the Kahrizak prison where they had been held.
Last December Iran said that it had charged 12 officersimplicated in the Kahrizak case.
Their trial was later reported to have started in March.
Iran's military courts are the ones that usually try policemen and military personnel.
A parliamentary investigation later found Saeed Mortazavi,a former Tehran prosecutor, responsible for the torture deaths of the three in Kahrizak.
There has been no word of any action to punish Mortazavi, who became the head of a government body tasked with fighting smuggling of goods.
The judiciary said that the court has studied cases of more than 60 other people over separate cases of mistreatment of protesters, and that 33 of them would go on trial.
Hundreds of protesters and opposition activists were arrested in the government crackdown following the disputed June 2009 election, which the opposition says Mahmoud Ahmadinejad, the president, won through massive vote fraud.
The opposition says more than 80 protesters were been killed in the post-election crackdown, but the government has confirmed around 30 deaths.
More than 100 protesters, activists and pro-reform opposition have been on trial, accused of fuelling the protests and being part of a plot to overthrow the government.