The Moscow City Court jury voted to acquit ethnic Chechens Kazbek Dukuzov and Musa Vakhayev in the killing of Klebnikov, which deepened concerns about media freedom in Russia, Vakhayev's lawyer Ruslan Khasanov said.
The announcement came at about 9 p.m., after a daylong court session during which jurors began deliberations following the trial, which was held behind closed doors. Dukuzov's lawyer Igor Korotkov said eight jurors favored acquittal and four were opposed.
Dozens of relatives and friends of the defendants burst into cheers, applause and tears of relief outside the courtroom. Dukuzov, 32, and Vakhayev, 42, walked quickly past reporters outside the courthouse shortly after the verdict was announced, and got into a white sedan that sped away.
"I am grateful to the entire Russian people," Dukuzov said before getting in the car.
Prosecutor Dmitry Shokhin said that the state might appeal the verdict, which he said was influenced by "gross violations" of procedural legislation.
Under Russian law, acquittals can be appealed.
"I am glad that in the Russian Federation they have finally introduced jury trials and that the jury made sense of this case and evaluated all the evidence," Khasanov said. Jury trials were introduced a few years ago.
Klebnikov was fatally shot on the street outside the Forbes office in Moscow in July 2004. The high-profile slaying raised questions about who would want to kill Klebnikov, a journalist and author who investigated corruption and sought to shed light on the closed, sometimes violent world of Russian business.
Prosecutors claimed the defendants killed Klebnikov on behalf of Khozh-Akhmed Nukhayev, a Chechen separatist figure who was the subject of a critical book by the victim, called "Conversations with a Barbarian," and remains at large.
The U.S. government and Klebnikov's family, whose roots are in Russia, have urged prosecutors to thoroughly investigate all angles and stressed the importance of bringing those behind the killing to justice, not just those who carried it out.
"We agree with the court decision because we respect the court. We were ready to agree with any decision of the court, regardless of our inner convictions, because we respect the decision of the court," said a lawyer representing the Klebnikov family, Larisa Maslennikova.
She would not say whether she believed the defendants were guilty.
Critics of Russia's justice system, which came under fire during the trial of tycoon Mikhail Khodorkovsky and is widely seen as lacking independence from the Kremlin, have said prosecutors failed to properly pursue other lines of investigation in the Klebnikov case.
The jury also acquitted Fail Sadretdinov, who was tried alongside Dukuzov and Vakhayev in connection with a separate crime, the alleged attempted murder of a businessman. Prosecutors said Sadretdinov was linked with the other two defendants in the attempted murder case.