Eric Chia said the case had cost him 11 years of his life
Eric Chia, the former head of state firm Perwaja Steel, was accused of approving fraudulent payments to a fictitious company in the 1990s.
But the court said the prosecution had failed to prove its case.
The verdict is a setback to Prime Minister Abdullah Ahmad Badawi's anti-corruption campaign.
Mr Chia is one of only two major figures to have been charged with corruption since Mr Abdullah came to power on an anti-corruption platform in 2003.
Mr Chia had close links to the administration of Dr Mahathir Mohamad, Mr Abdullah's predecessor.
Established in the 1980s to spearhead Malaysia's industrial development, Perwaja Steel came close to collapse after making heavy losses and accumulating debts of $2.6bn.
Mr Chia was accused of financial mismanagement by former deputy prime minister Anwar Ibrahim in 1996 and charged with criminal breach of trust in 2004.
Prosecutors claimed that he had overseen the transfer of 76.4m ringgits ($22m) in funds to a bogus company in 1994.
Mr Chia, who denied all wrongdoing, faced a maximum penalty of 20 years in jail if convicted. But the judge said the prosecution's case had been flawed.
"The prosecution's case has been negated by their own evidence and crippled by the non-calling of essential witnesses," said judge Akhtar Tahir.
Mr Abdullah was re-elected in 2004 on a pledge to tackle corruption in business and public administration but critics have accused him of being too timid and losing his way.
The BBC's Jonathan Kent in Kuala Lumpur said there had been few arrests of prominent figures and Mr Abdullah would have to redouble his efforts if he was to convince people of his commitment to addressing the problem.