Stockley, who was charged with first-degree murder in the 2011 shooting, had insisted he saw 24-year-old Smith holding a gun and felt he was in imminent danger. Prosecutors said the officer planted a gun in Smith's car after the shooting.
Stockley, 36, requested his case be decided by a judge alone.
"This court, in conscience, cannot say that the State has proven every element of murder beyond a reasonable doubt or that the State has proven beyond a reasonable doubt that the defendant did not act in self-defence," St Louis Circuit Judge Timothy Wilson ruled.
Assistant Circuit Attorney Robert Steele emphasised during the trial that police dashcam video of the chase captured Stockley saying he was "going to kill this [expletive], don't you know it".
Less than a minute later, the officer shot Smith five times.
Stockley's lawyer dismissed the comment as "human emotions" uttered during a dangerous police pursuit. The judge wrote that the statement "can be ambiguous depending on the context".
Stockley left St Louis' police force in 2013 and moved to Houston.
The case was among several in recent years in which a white officer killed a black suspect. Stockley said he found a revolver between the centre console and passenger seat of Smith's car.
But prosecutors questioned why Stockley dug into a bag in the back seat of the police SUV before returning to Smith's car.
The gun found in Smith's car did not have his DNA on it, but it did have Stockley's.
- AP