Forty-three-year-old Selek, known for her critical studies of the Kurdish conflict and of vulnerable communities in Turkey, was detained on suspicion of bombing an Istanbul spice market popular with tourists two days after the blast.
Accused of being a member of the Kurdistan Workers' Party, she was held in prison after she refused to give police the names of rebels she had met during her research, and then freed in 2000 after the publication of a report blaming the explosion on a gas leak.
Selek went on trial and was acquitted twice, in 2006 and 2008, before leaving Turkey for Germany and then France.
She was acquitted a third time in 2011 before being handed a life sentence at a new trial in 2013.
Friday's verdict marked her fourth acquittal, after the sentence was overturned earlier this year.
Supporters in France said the latest trial allowed Selek's lawyers "to emphasise all day the absurdity and arbitrariness of the procedure".
"One by one, they pointed out the false evidence that allowed the creation of a fictitious history of the blast to silence Pinar Selek and prevent her from continuing her sociological work among oppressed social groups."
The previous acquittals were based on the primary witness's retraction of his testimony and lack of evidence the blast was a bomb attack.