The Dutch side had been expected to qualify with ease through Group B when the draw pitted them against Ludogorets, Chornomorets and Dinamo Zagreb.
But their European adventure ended in embarrassing fashion, as a 1-0 defeat in their winner-take-all encounter to a 10-man Chornomorets outfit at the Philips Stadion sealed their fate.
Striker Dja Djedje's goal just before the hour proved their undoing, as he headed home Sito Riera's cross to send the Ukrainian club into the knockout phase.
And the visitors could even afford to play the final three minutes a man down after Riera was sent off for violent conduct, leaving PSV facing up to an eighth defeat in 12 games in all competitions that piles yet more pressure on under-fire boss Phillip Cocu.
In the other Group B game, Dinamo's winless campaign finished with a 2-1 defeat to Ludogorets, while over in Group A, Swansea City lost 1-0 at Saint Gallen but still advanced to the last 32.
Marco Mathys' strike 10 minutes from time gave the Swiss side their second win of the group stage, but Kuban Krasnodar's 1-1 draw with group winners Valencia meant that it mattered little.
British rivals Wigan Athletic were not as fortunate as Swansea, with two goals in 16 minutes either side of the break from Dejan Mezga and Zeljko Filipovic earning Maribor a come-from-behind 2-1 win and progression as Group D runners-up.
Neither team were able to catch Rubin Kazan at the start of the night, but the Russians did Maribor a favour by beating Zulte-Waregem 2-0.
The battle for top spot in Group E went the way of Fiorentina - the Italians winning 2-1 against nearest rivals Dnipro - while a 0-0 draw between Pandurii Targu Jiu and Pacos de Ferreira in Romania was meaningless.
Salzburg progressed as the winners of Group C courtesy of a 3-0 victory against second-placed Esbjerg, with Standard Liege losing 3-1 at home to Elfsborg.
Group F saw Maccabi Tel Aviv qualify with a 1-0 win against Bordeaux, while Frankfurt prepared for the knockout stages in style by beating APOEL 2-0.
A Roberto Soldado hat-trick made it six wins out of six for Tottenham in Group K as they beat Anzhi Makhachkala 4-1, with Lewis Holtby scoring in between with a clever left-footed finish to assert the Premier League side's dominance over the second-placed Russians.
Sheriff Tiraspol beat Tromso 2-0 in the other game in that pool, while elsewhere there were wins for Legia Warsaw - 2-0 against Apollon - and Maccabi Haifa - 2-1 against Shakhter Karagandy - as well as a 2-2 draw between already qualified PAOK and AZ, and a goalless stalemate between Lazio and Trabzonspor.
Lyon's 2-1 win over Vitoria Guimaraes combined with Real Betis' 0-0 draw against Rijeka gave the French side top spot in Group I, while Sevilla ended the night on top of Group H thanks to goals at the end of each half from Vicente Iborra and Raul Rusescu as they beat Freiburg 2-0.
The other game in that pool saw Slovan Liberec edge Estoril 2-1, sending the Czechs through, while Genk won 1-0 at Thun and Dynamo Kiev came from one down to beat Rapid Vienna 3-1 in Group G, taking their place in the last 32 at the expense of the Austrians.
