The brutal killing of the reporter, who worked for the small-circulation Novaya Gazeta newspaper, highlighted the risks run by journalists in Russia.
She was the 13th journalist to be killed in a contract-style killing in Russia during Vladimir Putin's period as president, according to the US-based Committee to Protect Journalists.
A former FSB (Federal Security Service) agent, Pavel Ryaguzov, was also acquitted by the jury of an extortion charge relating to the case.
A spokesman for the Organisation for Security and Co-operation in Europe (OSCE), which monitors media freedom in Europe, said after the verdict that Russia's failure to solve the murder of Ms Politkovskaya amounted to a "human rights crisis".
Most Moscow newspapers are savaging the Russian police, investigators and prosecutors for their failure to convict anybody for the murder, the BBC's Rupert Wingfield-Hayes reports.
The opposition daily Kommersant called the trial a complete failure.
Even pro-Kremlin newspapers accused Russia's law enforcement agencies of utter impotence in investigating the murder, our correspondent reports.
In Paris, the press watchdog Reporters without Borders said the trial had been marked by incoherence.
The US state department joined the chorus of calls for a new investigation into the murder.