The assassination attempt occurred close to Moscow on March 17, 2005 when a bomb exploded as Chubais' car was passing and his vehicle subsequently came under attack from men armed with automatic weapons.
Chubais was not hurt in the attack.
Alexander Naidenov, Robert Yashin and Vladimir Kvachkov were released in the courtroom after being found not guilty.
Vladimir Kvachkov, allegedly a key figure in the assassination attempt, said the verdict was "an act of civic courage."
He told reporters outside the court building he was not sure yet whether he would bring charges on the grounds of "unwarranted prosecution."
Chubais said he was unhappy with the verdict.
"I consider it a mistake," he said.
According to prosecutors, the defendants were motivated by their extremist views and a violent dislike of Chubais, an architect of economic reforms in the 1990s that impoverished millions and gave vast fortunes to a handful of well-connected oligarchs.
Chubais is currently behind a series of unpopular decisions to raise electricity tariffs.