Atletico's exit from the Champions League at the group stage was confirmed last week with a 2-2 home draw to Bayer Leverkusen.
The Rojiblancos still had the chance to claim a Europa League spot, but missed out on third place in Group B as they were beaten 2-1 by Porto.
Goals from Mehdi Taremi and Stephen Eustaquio put Porto in command, with a late Ivan Marcano own goal nothing more than scant consolation for Atletico.
The LaLiga club's defeat, combined with Bayer Leverkusen's goalless draw with group runner-up Club Brugge, means it is the Bundesliga side that drops into the Europa League.
For Atleti, the focus is now solely on domestic matters and ensuring it at least qualify for next season's Champions League, with the LaLiga title already looking a tall order.
Atletico, eight points behind LaLiga leader Real Madrid, heads out of Europe with just one win from six matches. It scored five goals and conceded nine, finishing bottom of a Champions League group for the first time in its history.