Jason Stockley, 36, was cleared on Friday of murdering Anthony Lamar Smith, 24, who was fatally shot after a police pursuit in 2011.
Daytime protests have been non-violent, but tensions have escalated overnight.
St Louis Police said some officers had chemicals and rocks thrown at them.
Their injuries were described as "minor or moderate" and the perpetrators as a "group of criminals".
"Today we saw again the vast majority of protestors are non-violent," St Louis Mayor Lyda Krewson said.
"But for the third day in a row the days have been calm but the nights have been destructive."
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Police posted images to Twitter of weapons reportedly confiscated in the city.
The protests began on Friday immediately after the court verdict. Weekend concerts by the Irish rock band U2 and British artist Ed Sheeran were cancelled due to security concerns.
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