Bates Battaglia broke a 3-3 tie with 5:09 left in regulation and J.F. Racine finished with 34 saves as Toronto wrapped up the fourth and final playoff spot in the North Division with a 5-3 win in Rochester on Wednesday.
The Amerks rallied from an early two-goal deficit, but the loss also means they will miss the Calder Cup Playoffs for the first time since 1989.
Brett Englehardt and Aleksander Suglobov gave the Marlies a 2-0 lead less than nine minutes into the game, but Michael Ryan, Chris Thorburn and Daniel Paille gave Rochester the lead heading into the second intermission.
Tyler Beechey tied the score, and Battaglia netted the game-winner, his 19th goal of the season, at the 14:51 mark of the third.
Rochester, needing a regulation win to keep its postseason hopes alive, pulled goaltender Jean-Marc Pelletier for an extra attacker with three minutes remaining, but Racine and the Marlies held on to win.
Elsewhere on Wednesday: