An unguarded Opara executed a close-in header off a pass from Graham Zusi on the winning play, which Columbus goalkeeper Matt Lampson had no chance to stop.
Second-place SKC (15-10-6) remained four points behind Eastern Conference leader New York with a chance to clinch a post-season berth.
The Crew (12-15-5), meanwhile, saw their late-season playoff push come to a likely end with the loss, which followed four wins in five games under interim head Coach Brian Bliss.
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