Retired general Levent Ersoz, 60, has been on trial since October last year accused of attempted murder.
The court ruled there was not sufficient evidence against Ersoz and decided to acquit him, his lawyer Hulusi Coskun told AFP.
"This trial should have never taken place. We have demanded his acquittal since the very beginning," he said.
Ersoz had already been convicted and jailed last year in one of the conspiracy cases against an array of figures accused of trying to topple Turkey's Islamic-leaning government.
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Ozal became Turkey's eighth president in 1989. When he died in office aged 65, the cause of death was given as heart failure.
His remains were exhumed from his mausoleum in October 2012 after prosecutors issued a warrant for toxicology tests.
A belated autopsy was requested following a presidential report that ruled the death was "suspicious", citing the absence of an investigation and missing blood test results.
Family members have long believed that Ozal, an ethnic Kurd who was seeking a negotiated solution to the conflict with Kurdish separatists in the southeast when he died, was poisoned.
The indictment against Ersoz was based on complaints from Ozal's widow and son who accused the retired general of having "led an assassination attempt against the president" -- a crime punishable by life imprisonment.
Ozal had implemented liberal economic policies during his tenure and supported the US-led intervention in Iraq during the Gulf war in 1991.