Matias Perez Garcia won control of a free kick from beyond midfield and laid it off to Atiba, who sent a laser into the left corner of the net to earn the point for San Jose (6-12-11).
Gabriel Torres opened the scoring for the Rapids (8-14-8) in the 84th minute with a chip off Chris Klute's cross from the right flank. Goalkeeper Jon Busch deflected the shot, but it curled just inside the post.
Both teams are winless in 10 games.
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