It had earlier appeared Celtic were safe, but the Polish side left it until almost closing time at the Court of Arbitration for Sport (CAS) before filing their appeal against UEFA's decision that expunged them from the elite club competition.
Legia beat the Scottish champions 6-1 on aggregate in the third qualifying round, but a second-leg 2-0 victory in Edinburgh was revised as a 3-0 win for Celtic after it emerged the Poles had fielded an ineligible player, Bartosz Bereszynski, as a late substitute.
That allowed Celtic to take the tie on away goals and step up preparations to face Maribor in Slovenia next Wednesday in the play-offs, while Legia were set for a Europa League clash at Aktobe in Kazakhstan on Thursday.
UEFA's appeals body on Thursday upheld the decision by its disciplinary body to award Celtic the 3-0 second-leg win.
However Friday evening's twist means the saga is not yet over.
CAS said in a statement: "The Court of Arbitration for Sport registered today at 17:30 a statement of appeal filed by the Polish club Legia Warszawa against the decision of the UEFA appeals body confirming the result 3-0 (forfeit) in favour of Celtic FC against Legia in the second leg of the third qualifying round of the UEFA Champions League. The UEFA considered that Legia had fielded an ineligible player (Bartosz Bereszynski) during the match.
"Legia requests urgent provisional measures from CAS allowing the Polish club to participate in the play-offs of the Champions League (20 & 26 August 2014). More generally, the club requests that the UEFA decision be set aside and that all sanctions against the club and the player Bereszynski be annulled.
"The CAS has immediately initiated an arbitration procedure and the respondents UEFA and Celtic FC have been invited to file written observations. A decision on request for provisional measures is likely to be issued on Monday 18 August around 18:00 (Swiss time)."
Legia failed to register Bereszynski in their squad list for the second qualifying round against St Patrick's.
That meant his three-match suspension had not officially been served when he came on as an 86th-minute substitute as Legia beat Celtic at Murrayfield.
Legia player Henrik Ojamaa declared the punishment excessive as he was unveiled at Motherwell following his loan move.
Ojamaa, who was on the bench for both games, said: "At the end of the day everybody understands that rules are rules but everybody feels the punishment was very excessive.
"It's a UEFA decision and the responsibility lies with them. The club realise that they made a mistake but the point was the punishment shouldn't be as severe because the team have done very well to get through convincingly and to get that taken away from them is obviously a big disappointment."
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