Ma was acquitted of leaking secrets and of defamation. He will face a new trial after state prosecutors brought fresh leaks charges against him earlier this month.
"Defendant Ma Ying-jeou is found not guilty" of violating the Communication Security and Surveillance Act and the Personal Information Protection Act, said Judge Wu Yung-yi.
Ma was not present when the verdict was announced. Throughout the trial he had denied any wrongdoing.
Ma was also accused of defamation by implying that the lawmaker had sought to influence a court case which he (Ker) was facing.
The judicial probe was investigating whether the parliamentary speaker at the time -- a political rival of Ma -- had improperly influenced the case against Ker in an attempt to benefit the lawmaker.
While still in office Ma had immunity from prosecution. But since he stepped down in May last year after serving the maximum two terms, the 66-year-old has been hit with a series of corruption and other allegations.
The KMT hailed today's ruling and urged lawmaker Ker not to appeal the case to avoid "political name-smearing and wasting judicial resources".
But Ker's lawyer Zan Keng-goan expressed shock at the verdict and vowed to appeal.
The leaks controversy sparked a political storm in 2013 and saw two top officials resign, while thousands of protesters took to the streets to demand Ma's resignation.
The DPP, then in opposition, compared the probe to the Watergate scandal in the United States, as information allegedly implicating the parliamentary speaker was obtained by a wiretap on lawmaker Ker's phone.
Chen was indicted after leaving office and had been serving a 20-year sentence for corruption until he was freed on medical parole in 2015.
However, Ma's popularity plummeted during his eight years in power, with public disquiet at policies seen as linking the island too closely to China and benefiting big business rather than ordinary people.
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