The French side were leapfrogged by Salzburg in Group F and a home win over already-qualified Athletic Bilbao in their final match in two weeks might not be enough for Kombouare whose side lost 3-0 at Ligue 1 rivals Olympique Marseille at the weekend.
The coach kept his job when big-spending Qataris took over at PSG in June but there have long been rumblings they want to replace him with a bigger name and his largely second-string side did him no favours in Austria.
Jakob Jantscher was completely unmarked at the far post when he swept in a 20th-minute opener for Salzburg and an injury-time goal by Dusan Svento meant the hosts, who next visit also-rans Slovan Bratislava, went above PSG with a better head-to-head record.
The long-time record scorer in the Champions League thanks to his exploits with Real Madrid, Spaniard Raul netted his first of the season in the continent's second club competition in Schalke's 2-1 home win over Steaua Bucharest in Group J.
His 57th-minute goal after Klaas-Jan Huntelaar's shot was blocked also meant the Bundesliga side secured top spot with one match to spare after Maccabi Haifa's surprise 2-1 defeat at AEK Larnaca, which leaves the Israelis waiting to qualify.
"We played very well in the first 25 minutes but for all our corners we did little with them," Schalke coach Huub Stevens told reporters.
"In the second half we showed what we are all about," he added of the 1997 UEFA Cup winners.
Lokomotiv powered to a 3-1 home win over Sturm Graz to seize Group L's second qualification spot and knock out the Austrians.
Anderlecht had already gone through but beat bottom side AEK Athens 2-1 away to make it five wins from five, meaning they will host the Russians on December 14 in a fight for first place and a better seeding.
LATE RED
Group E leaders Stoke City needed a Kenwyne Jones header after 81 minutes to draw 1-1 at home with Dynamo Kiev and secure their passage to the next round for the first time.
Ricardo Quaresma struck twice, including the winner in stoppage-time, to put Besiktas on the brink of qualification from Group E with a 3-2 victory at Maccabi Tel Aviv.
Fulham, the 2010 runners-up, lost 1-0 in the rain at already-through Twente Enschede to miss the chance to progress and need a point at home to OB Odense in their last Group K game.
Striker Andy Johnson will be suspended against Odense after receiving a late red card at Twente.
Third-placed Wisla Krakow prevailed 2-1 at eliminated Odense to move a point behind the English side with group winners Twente travelling to Poland next.
Romanians Vaslui and Italian side Lazio remain locked together on six points after a 0-0 stalemate
