But to the fury of many of the victims and their families, it rejected claims for compensation on the grounds that all reparation issues had been settled at a government level by international peace treaties.
With the public gallery packed with the plaintiffs' supporters holding photographs of the dead, Koji Iwata, the presiding judge of the Tokyo district court, said the imperial army had contravened the Geneva and Hague conventions by spreading plague, typhoid and other diseases in Quzhou, Ningbo and Changde between 1940 and 1942.
"The evidence shows that Japanese troops, including Unit 731 [the secret experimental unit] and others, used bacteriological weapons on the orders of the imperial army's headquarters and that many local residents died," he said.
His terse judgment ended a five-year case, filed by 180 mostly Chinese plaintiffs who were seeking about £55,000 each in damages for the suffering caused by Unit 731.
But the landmark confirmation of the germ warfare programme is an embarrassment to the government, which has long dismissed allegations concerning Unit 731 for lack of evidence. For many years, school textbooks were barred from mentioning even the unit's existence, but the plaintiffs' lawyers said the verdict would change perceptions.
"The court's recognition of the facts will make it impossible for bureaucrats and politicians to deny what happened ever again," said Kohken Tsuchiya, the head of the plaintiffs' legal team. "This is positive even though compensation was denied."
In a written summary of the 28 hearings and hundreds of pages of evidence, the three judges of the Tokyo district court said they were in little doubt that the spread of deadly pathogens in Manchuria were caused by Unit 731's facility at Harbin. That facility - established in 1938 by General Shiro Ishii under the innocuous name of the epidemic prevention and water supply unit - led the world in the science of germ warfare thanks to its inhumane methods.
"Its main purpose was to research, develop and produce biological weapons," said the ruling. "In order to do this, prisoners from the Chinese resistance forces were used as the subjects for experiments."
During the five-year court case, Unit 731 veterans confessed to taking part in vivisections of live victims, cultivating anthrax, typhoid, cholera and other viruses, and dropping plague-infected fleas over villages.
Elderly plaintiffs flew from China to testify - often in tears - about their communities being ravaged by diseases that spread mysteriously after Japanese planes flew low overhead and dropped wheat, rice or cotton infested with fleas.
After the war, the Japanese army burned most of the facilities used by Unit 731 and the United States granted immunity to Ishii and his colleagues in return for their research findings. As a result, no mention was made of their activities during the Tokyo war crimes tribunal.
Yesterday's judgment filled only part of the hole left by that omission. Historians estimate that the biological warfare death toll may have been as high as 300,000, but the plaintiffs requested compensation for only 2,100 people for whom they could provide names, addresses and dates of death.
Despite the long-awaited legal recognition of Unit 731 atrocities, many plaintiffs expressed anger that their compensation claims were rejected. "I'm furious," said Chen Zhifa, a frail 71-year-old who saw his father and elder brother die in agony after the plague struck their home in eastern Zhejiang province. "Biological weapons aren't like ordinary bombs. The impact grows and so does the suffering long after the first attack. But today, the judge dismissed our claims in five minutes."
The plaintiffs said they would appeal, but precedent suggests they have little chance of success. Japanese courts have rejected all of the dozen or so previous lawsuits filed against the government by individuals such as former "comfort women" sex slaves, or prisoners of war.
Wang Xuan, a spokeswoman for the plaintiffs, said they would fight on. "This verdict is an absurd paradox. The judges accepted a serious crime against humanity and a tragedy for Chinese people had occurred, but they said Japan didn't have to take responsibility. What kind of justice is that?"