Atlanta United did not qualify for the Eastern Conference playoffs after a 2-1 loss at the Columbus Crew on Sunday in the regular season finale.
Columbus finished third by having the tiebreaker over Orlando City in wins per game.
The Crew will host the New York Red Bulls in a single-elimination match later this month.
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In a tumultuous four minutes for Atlanta, the Five Stripes went from possibly leading to trailing 1-0. It began when Atlanta leading scorer Jon Gallagher drew a penalty on Crew goalkeeper Eloy Room in the 24th minute.
Gallagher got behind the defense and forced Room off the line and in attempting to reach the ball he tripped Gallagher. The play went to video review and the PK call on the field was overturned.
Given a reprieve, the Crew took the lead on Zelarayan's sixth goal in 16 games this season. Quick passing led Milton Valenzuela to leave the ball at the top of the box. Zelarayan made several moves to gain space and put a chip shot over Brad Guzan.
Zardes made it 2-0 in the 55th on the counter when he got on the end of a ball from the back on the left flank to score his 12th goal.
Atlanta pulled to within 2-1 five minutes later when the Five Stripes got a penalty call that stood after Valenzuela fouled Jurgen Damm. Moreno converted for his first goal in his 14th match.
The Five Stripes' Franco Escobar received his second yellow card in the 90th minute and was ejected.