Rookie defender Jalil Anibaba scored his first two career goals — both in the first half — for the Fire (9-9-16), who won for the seventh time in their last 10 games but still missed the postseason.
Emilio Renteria got his eighth goal in the 73rd minute and Dilly Duka tied the score in the 79th for the Crew (13-13-8), who missed out on securing the Eastern Conference title and homefield advantage. Columbus, now third in the East, could fall into a wild-card spot pending results of Sunday's games.
Anibaba's first goal came in the 11th minute as he skipped a shot off his head past Crew goalie William Hesmer. He scored again in the 29th on a similar play following a long feed from defender Cory Gibbs.
The goals broke a seasonlong drought for Anibaba, who last scored in a U.S. Open Cup tournament game in March.
Chicago goalie Sean Johnson turned shots three shots while Hesmer had five saves for Columbus.