The Polish champions had contested the decision by the Control, Ethics and Disciplinary Body to forfeit their 2-0 victory in the second leg of their third qualifying round tie with the Parkhead club, awarding Celtic a 3-0 victory because Legia had fielded an ineligible player, Bartosz Bereszynski.
That made the aggregate between the clubs 4-4, and Celtic went through on the away goals rule. At an appeal hearing at Uefa's headquarters in Nyon, Switzerland, Legia argued it had been an administrative error which saw them include the player who was still serving a suspension from last season, and not befitting the level of punishment it brought.
However, Uefa's rules on suspended players are clear, and a 3-0 forfeit is the automatic sanction. Legia are now planning to take the case to the Independent Court of Arbitration for Sport in a last-gasp attempt to be reinstated to the Champions League play-offs, which kick off next week.
Club owner Dariusz Mioduski wrote on Twitter: "Unfortunately for now football is not winning... We are going to CAS."
However, it is considered unlikely any case would be heard ahead of Celtic playing Maribor in Slovenia on Wednesday, or that CAS would attempt to have the tie delayed to give them time to call and decide upon the case.
Legia are scheduled to face Kazakhstan side Aktobe in the play-off round for the Europa League a week tonight.
And, while their owners are vowing to take the case as far as they can, the decision by Uefa appears to have been their best chance of forcing their way back into the Champions League.
The verdict was confirmed in a UEFA statement which read: "The UEFA Appeals Body met yesterday following an appeal by Legia Warszawa against the decision taken by the UEFA Control, Ethics and Disciplinary Body on 8 August.
"The appeal lodged by the Polish club was rejected and, therefore, the original decision of the UEFA Control, Ethics and Disciplinary Body is confirmed.
"The Control, Ethics and Disciplinary Body had sanctioned Legia for fielding a suspended player (Article 18 of the Regulations of the UEFA Champions League, 2014/15 competition, and Article 21 of the UEFA Disciplinary Regulations, 2014 edition) in the 2014/15 UEFA Champions League third qualifying round return leg against Celtic FC in Edinburgh on 6 August. That match has been declared as a forfeit, meaning Legia lost 3-0."
Legia president Boguslaw Lesnodorski echoed Mioduski's pledge to take the matter to the Court of Arbitration for Sport.
He wrote on Twitter: "Negative decision, it's hard even to comment, we are using the CAS (we plan to tomorrow) and otherwise we are focused only on the games."
Mioduski released a statement through the club's official website which stressed Legia's determination to keep fighting for Champions League reinstatement.
The statement read: "Till the last moment we hoped that the spirit of sport wins, we find the decision extremely unfair.
"However we expected that decision and were prepared for it. We are to appeal to the CAS promptly.
"We will use the full appeal procedure, in order to get back our result that was fairly gained on the pitch.
"We will certainly fully subordinate to the final verdict. But I still hope that football will win, as well as the values it is based on: fair-play and respect to the on-the-pitch result."
Lesnodorski added: "We hope that CAS will judge our case as soon as possible.
"We don't give up and keep fighting. Our lawyers are now working hard on the case, while the team prepares for the forthcoming matches. We aim high as always."
Before the verdict, Hoops manager Ronny Deila spoke only about facing Maribor in the play-off.
He said: "We have prepared for Maribor. They are a good team and they have been the champions of Slovenia in the last three years.
"There is nothing easy in the Champions League so it is going to be a hard game but we know what we are able to do when we are at our best.
"It is hard to say if they are better or worse (than Legia Warsaw) but they are a good team.
"Legia was a good team as well, so nothing is easy but we can do much better than we did against Legia and we will play at Celtic Park and those two things can be good for us.
"I have seen European nights at Celtic Park and I understand why you get results there and that's because you have unbelievable fans behind you."
Meanwhile, Ronny Deila knew Maribor had a spy watching his side defeat St Johnstone 3-0 at Perth - but he reckons he may be an agent of misfortune.
For the Hoops boss reckons it was a wasted journey for the man from Slovenia after seeing his players turn in a Jekyll and Hyde performance.
Deila will be taking his team to Maribor for the first leg, and has had them closely watched. But he is unsure what their spy in the stand will have made of what he saw at McDiarmid Park.
Deila reflected: "We did some good things, but there are other things we have to do much better.
"We have had Maribor watched, and it's going to be an exciting game. But first we have to concentrate on Saturday when we play Dundee United."
Deila is relieved to be going into that game when the league flag will be unfurled with three points on the board, and a first Premiership win under his belt.
And, just four days before they return to European action, Deila does not want the occasion to fall flat. He said: "We're going to go into that game with hunger and the right attitude. We'll do everything we can to deliver a good performance."
Deila will have Charlie Mulgrew back from suspension for that game, and Leigh Griffiths, if the striker has recovered from the illness which the manager revealed kept him out last night.
But the prospect of James Forrest getting further game time ahead of the Maribor ties is even more heartening for the Norwegian.
Deila said: "Every team wants a James Forrest. He's very important to our team. But he needs matches, and that's why he only played 58 minutes against St Johnstone. We have to take care of him to make sure he doesn't get injured."
Deila elected to go with Craig Gordon at Perth.
But even though Lukasz Zaluska saw his long-waited chance to become No.1 following the sale of Fraser Forster slip from his grasp, the manager has encouraged the Polish keeper not to let his head drop.
"It is hard, and Lukasz will feel sorry he was not selected because he is a good player," said the manager.
"But I've seen good things in Craig, and he played well in this game."