Houllier bemoans "outrageous" penalty
Emile Heskey had given Liverpool a first-half lead before Marseille came from behind to make the Premiership side pay for having Igor Biscan sent off.
Biscan saw red for tugging Steve Marlet's shorts and Didier Drogba equalised from the penalty spot.
In the second half Abdoulaye Meite's header gave Marseille victory, although it was Liverpool's depleted forces who battled away until the final whistle for the equaliser which would have taken them through.
And it was a double blow for Liverpool, with striker Michael Owen having to go off with what Houllier described as a "tight hamstring" and one which "could keep him out of the national team next week".
"The referee's decision had a major influence on the outcome of the game. It was outrageous," claimed Houllier.
"It came at a time when we were on top and their crowd were beginning to turn on them. No one seemed to appeal I thought it was a goal kick.
"I felt the incident was three or four yards outside the box and the referee actually played advantage. What would be have done had they scored?
"It was a dubious decision and one that changed the game.
"I feel sorry for my players, I could not have asked for more from them after that, and I feel sorry for the fans who travelled to support us having to see that decision.
"If we had been dominated, I would have said, okay, but we were in control and would have gone on to win.
"It was a very generous decision, a home penalty and one that I doubt would have been given the other way.
"I saw something happen, but it was well outside the box and maybe should have been just a free-kick but a penalty and a red card is two bad decisions."
Liverpool's last chance of silverware went with last night's defeat and they now will turn all their attention to securing fourth spot in the Barclaycard Premiership and with it a place in next season's Champions League.
Houllier added: "I have joked recently that it is not players that get you the sack, but referees and that referee has dealt a bad blow for Liverpool Football Club."
Marseille boss Jose Anigo insisted the penalty decision and the red card for Biscan were correct.
He said: "When you are the last player and you commit a foul like that then the rules say you will be sent off.
"It is the referee's decision, not mine, sometimes they go for you and sometimes against. You just have to respect what the referee says."
He added: "It was a great victory for us, and for a young coach like me. It has been the best result I have had as a coach.
"As far as playing Inter Milan next, I have thought hard about playing Liverpool, now I want to enjoy this moment before I start worrying about Italians."
: Barthez, Ferreira, Dos Santos, Meite, Beye, Flamini, Hemdani, N'Diaye, Batlles (Mido 71), Drogba, Marlet (Meriem 79).
: Dudek, Carragher, Riise, Hyypia, Biscan, Kewell (Sinama Pongolle 82), Murphy (Cheyrou 69), Hamann, Gerrard, Heskey, Owen (Baros 62).
: A Dauden Ibanez (Spain).
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