The acquittal comes amid renewed scrutiny on government corruption with Prime Minister Anwar Ibrahim, who took office in November last year, ordering a review into the previous administration's projects in a bid to root out graft.
Najib, who is serving a 12-year prison sentence after being found guilty in a separate case, was charged in 2018 with abusing his position as prime minister to amend a government audit into the multibillion-dollar scandal at 1Malaysia Development Berhad (1MDB).
The fund's former chief executive Arul Kandasamy was charged with abetting Najib. Arul and Najib both pleaded not guilty.
On Friday, the Kuala Lumpur High Court ruled the prosecution had failed to establish a case against them, their lawyers told reporters.
"(The court) found that there was no element of gratification... absolutely no element of corruption in Najib's role in these charges," Najib's lawyer Shafee Abdullah said.
Arul, who was present at the news conference, said he felt vindicated by the court decision, adding that he had been "honest and straightforward" about his role at 1MDB.
The Attorney-General's Office did not immediately respond to a request for comment.
Malaysia's 1MDB is the subject of corruption and money-laundering investigations in at least six countries.
An estimated $US4.5 billion ($A6.7 billion) was misappropriated from 1MDB by high-level officials of the fund and their associates between 2009 and 2014, the US Justice Department has alleged.
Najib is facing three more cases related to corruption at 1MDB and other state entities.
He has also sought a judicial review against his conviction in a 1MDB-linked case, with Malaysia's highest court expected to decide on the application this month, according to local media.
Other Malaysia politicians facing corruption charges include deputy premier, Ahmad Zahid Hamidi, the leader of Najib's coalition Barisan Nasional.
Zahid has pleaded not guilty to 47 charges of corruption and money laundering.
Barisan is a key partner in Anwar's administration, which needed its support to form a government after a divisive election last year.
