The Ireland striker turned up for the flight to Romania at Glasgow Airport despite feeling unwell, but club medical staff decided he was too ill to travel.
The last-minute development is a huge blow to manager Ronny Deila, who is already missing top goalscorer John Guidetti as well as injured attacking players Kris Commons and James Forrest.
Guidetti has scored nine goals in nine games since arriving on loan from Manchester City but the deal was not completed in time for him to be registered in time for Europe.
Stokes has started the last two Europa League games, including the 2-1 home win win over Astra which saw his fellow forward Stefan Scepovic score. Leigh Griffiths is another option for the Norwegian manager.
Deila is expected to restore Craig Gordon to his starting line-up. The Hoops goalkeeper missed the Premiership win over Inverness last weekend with a knee complaint but assistant manager John Collins confirmed that Gordon has travelled to Romania.
Gordon has been in superb form for Celtic, who sit second in Group D with seven points from three games following their 2-1 win over Astra Giurgiu in Glasgow last month.
“He is back training yesterday and available for selection,??? said Collins. “There are no easy games in Europe, there are no poor teams and the keeper has been called upon and done very well.
“They have some good football players, they move the ball well and if we are not on our toes they will create chances.
“A win would put us in an excellent position, with 10 points, a very strong position going into the last two games but I don’t think anything would be guaranteed.”
Collins confirmed that Aleksandar Tonev will also travel. The Bulgarian missed the Inverness match after an appeal against his ban for racial abuse was not submitted in time.
The Hoops winger – on loan from Aston Villa – was suspended by the Scottish Football Association for seven matches for using “offensive, insulting and abusive language of a racist nature” towards Aberdeen defender Shay Logan when the two teams met in September.
Collins confirmed that the Parkhead club would appeal but was reluctant to be drawn on the issue.
He said: “I don’t want to get involved in that. I am not allowed to comment. We will back Aleksandar.
“I am led to believe the appeal will go in. Training has been normal. Obviously he is disappointed with the verdict but he has to focus on his football.
“There is no concern, he will be available. He will be desperate to play, like all the rest of the players.”