According to the appellate court, much of the witness testimony was not credible because it was unclear on dates, locations and often contained elements that could be "objectively proven to be impossible".
The court ruled that a conviction on such evidence would be "built on quicksand".
The ruling is a blow for prosecutors who had appealed for a stiffer sentence and sought an additional conviction for war crimes for Kouwenhoven.
Taylor was questioned last month over his alleged link with Kouwenhoven but he refused to testify about his relationship with the Dutch businessman.
The former Liberian president is being held in a prison in The Hague, after his trial before the Special Court for Sierra Leone was moved to the Netherlands amid fears that his presence in Freetown could threaten security in the region.
Taylor faces charges of controlling armed militia in neighbouring Sierra Leone that had murdered, raped and tortured civilians during the country's 1991-2001 civil war.