The 47-year-old former international defender was replaced on an interim basis by technical director John Hackworth on an interim basis.
City ranks 12th in the Western Conference on 19 points, nine points out of a playoff spot.
Carnell guided City to last year's Western Conference regular-season title at winning 17, drawing three and losing 12 in the club's inaugural season. But St. Louis was swept by Kansas City in the first round of the playoffs.
"Given Bradley's many contributions to the club, this was not an easy decision," City sporting director Lutz Pfannenstiel said.
"Unfortunately, based on our year-two results to date, we believe a coaching change is in the best interest of the club as we regroup and look to improve both our performance and our results."
Hackworth went 20-23 with 14 drawn from 2012 to 2014 with the Philadelphia Union and has had various coaching roles with US national youth teams.
His first match guiding City will come on Wednesday when league doormat San Jose visits St. Louis.
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