Fifteen-year-old Maina Sunuwar was tortured and killed after she was detained by the army in 2004 for alleged links to Maoist rebels.
But a military tribunal the following year ruled that her death was accidental and charged the three soldiers involved in the case with only minor offences.
Maina's mother brought a case in a civilian court which delivered its verdict yesterday, a court official told AFP.
A fourth soldier, the most senior of all those accused, was acquitted.
"We have fought for justice for so many years, I'm glad the court has understood our plight," Sunuwar's mother Devi told AFP.
"But our fight is not over. I'm worried the decision might be limited to paper. The state must implement the court's decision."
Devi campaigned for years for justice for her daughter, who was arrested when soldiers came to their home looking for her mother.
"We believed that Maina had been taken, and perhaps killed, only to punish her mother," said Advocacy Forum Nepal, a legal rights group, in a report about the long-running case.
A military tribunal in 2005 found that Sunuwar had been repeatedly held under water and given electric shocks to her feet and wrists during interrogation.
But it ruled that her death was accidental and the three soldiers named in the case were only charged with minor offences, including using improper interrogation techniques and failing to follow procedure.
In 2007 the case was taken to the Supreme Court and an arrest warrant was issued the following year for the three soldiers and a major.
The major, Niranjan Basnet, who was found innocent yesterday, is the only one of the accused still serving in the army, which has been repeatedly accused by activists of sheltering its men from prosecution.
"There is a worry, despite winning the case after so many years, the convicted might still not go behind bars," said Mandira Sharma, a human rights lawyer and activist who worked on the case.
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