Liverpool, who had won their opening seven matches, twice took the lead in their final group-stage game in the Netherlands, only to suffer a 3-2 defeat.
Despite the loss, Barcelona’s failure to beat Atalanta meant Arne Slot’s side finished top of the group with 21 points, two clear of their closest rivals.
The match was full of action, starting with Cody Gakpo converting a penalty in his home city against his former club after Joey Veerman fouled Federico Chiesa.
PSV quickly responded, with Johan Bakayoko equalizing after a brilliant turn and finish. Liverpool regained the lead through Harvey Elliott, who pounced on a parried shot from Chiesa.
But PSV turned the game around, with goals from Ismael Saibari and Ricardo Pepi handing Liverpool their first European defeat of the season. The Reds ended the match with 10 men after substitute Amara Nallo was sent off in the 87th minute for a foul on Bakayoko.
With a spot in the last 16 already secured, Slot rotated his squad ahead of Saturday’s crucial Premier League clash at Bournemouth.
PSV finished 14th in the 36-team table, securing a place in the playoffs.
Liverpool’s last-16 opponents will be the winners of a play-off between Paris Saint-Germain, Benfica, Monaco, and Brest.