Protesters displayed their support for conscripts who are often subject to brutal abuse by their elders in the troubled Russian military.
Some held posters or shouted slogans criticising the military leadership and calling for the resignation of officials including Defence Minister Sergei Ivanov and President Vladimir Putin.
The demonstrators did not have the required permission for the protest, and several dozen police stood by. Some waded into the crowd in downtown Moscow and spoke with demonstrators, who dispersed peacefully after about two hours.
A few dozen people held a similar demonstration in the Ural Mountains city of Yekaterinburg, the capital of the home region of the victim, Andrei Sychev, Ekho Moskvy radio reported.
Prosecutors say Sychev, an 18-year-old private at the Chelyabinsk Tank Academy in the Ural Mountains region, was beaten and tortured on New Year's Eve, causing severe injuries and a gangrenous infection that led to the amputations.
Several other soldiers were beaten in the same incident, but they sustained lighter injuries.
Mr Ivanov, who was unaware of the incident until this week, ordered an investigation yesterday into why military officials failed to report it immediately and said seven soldiers have been detained.
He also fired the head of the tank academy, who was charged with abuse of office for allegedly concealing the crime.
Sychev was not hospitalised until several days after the beating, when he was already in critical condition.
Public anger has mounted over the incident and it has damaged the reputation of Mr Ivanov, seen as a potential successor to Mr Putin in
2008 elections.
"There have been worse times, but none more despicable," a homemade sign held by a woman at the Moscow rally said. Rights groups accuse military officials of condoning vicious bullying as a means to maintain discipline.
All Russian men between the ages of 18 and 27 are required to serve at least two years in the armed forces, though many avoid the draft through exceptions or bribery.