Atletico Madrid were knocked out of Europe altogether following a 2-1 loss to Porto in the Champions League.
They hoped to reach the Europa League after Champions League elimination last week in a draw with Bayer Leverkusen.
But goals from Mehdi Taremi and Stephen Eustaquio saw Porto win despite Ivan Marcano's own goal in added time.
It is the first time Diego Simeone's team have finished bottom of a Champions League group since he took charge of the La Liga side in 2011.
Bayer Leverkusen's 0-0 draw with second-placed Club Bruges pushed Atletico to the bottom of Group B on their head-to-head record with the German club.
The two previous times they were knocked out in the Champions League group stage - in 2009-10 and 2017-18 - Atletico went on to win the Europa League.
Pressure is mounting on long-serving Simeone, with his side having only four wins in their past 12 games in all competitions.