The unanimous not-guilty verdicts came in a trial compromised from the start by the absence of the suspected gunman and any alleged mastermind behind the politically charged October 2006 killing. Prosecutors vowed to appeal.
The judge said the defendants were free to go, and they burst out of a courtroom cage and embraced relatives.
Ethnic Chechen brothers Dzhabrail and Ibragim Makhmudov and a former Moscow police officer, Sergei Khadzhikurbanov, were accused of helping organize and arrange Politkovskaya's contract-style killing. All three were charged with murder and could have been imprisoned for life if convicted.
Politkovskaya's probing reports on atrocities in Chechnya and abuses by Russian authorities angered the Kremlin but won her international acclaim. Her shooting shocked the world and widened the rift between Moscow and the West, underscoring the risks run by independent journalists and government critics while hardening the Kremlin's depiction of Russia as a nation beset by foes.
The female captain of the 12-member jury read out the verdicts after about two hours of deliberations at a military courthouse on Moscow's main pedestrian souvenir-shopping street, the Old Arbat. When the judge repeated that the defendants were acquitted, relatives of the Makhmudov brothers broke out into clapping and cries of "Bravo!"
"Thank God, thank the jury," said Ibragim Makhmudov, still in the courtroom cage shortly after the verdict. "There was no other possible outcome."
"We're glad," said defense lawyer Murad Musayev. "This is something that happens rarely in Russia. This is what I call justice."
But relatives and former colleagues of Politkovskaya have said that regardless of the verdict, justice will not be served until the triggerman and the mastermind who had her killed are prosecuted.
The defendants are accused of helping organize and arrange the attack, but the suspected gunman - a third Makhmudov brother, Rustam - is said to be hiding abroad, and prosecutors have not named anyone believed to have ordered her killing.
"Everything is still ahead - the investigators now have to start a proper investigation," said Karinna Moskalenko, a prominent lawyer who represented Politkovskaya's family at the trial. "The more time goes by, the harder it gets."
Politkovskaya was shot in the elevator of her Moscow apartment building on Oct. 7, 2006, as she returned from a supermarket with groceries.
Dzhabrail Makhmudov was accused of driving his brother Rustam to the building. Prosecutors say Ibragim Makhmudov warned of Politkovskaya's impending arrival with a telephone call to Dzhabrail. Khadzhikurbanov allegedly planned details of the attack, recruited the Makhmudov brothers and acquired a pistol with a silencer for the shooting.
In final arguments Tuesday, Musayev accused the prosecution of fabricating evidence and dismissed their case as "dust, fluff and ash."
Juries in Russia acquit defendants far more often than judges, who critics of Russia's justice system say are stuck in the Soviet tradition of presumed guilt. Jury acquittals can only be appealed on technical grounds, but prosecutor Vera Pashkovskaya said the judge had committed numerous procedural violations and said the state intends to appeal.