The Catalan side, part-owned by the City Football Group of Premier League champions Manchester City, thought they had been handed a lifeline when they were awarded a penalty and Levante defender Coke was shown a red card for a foul.
But the decision was overturned following a VAR review and Levante were given a free kick instead.
Girona were then dealt more pain when Levante's Macedonian striker Bardhi raced into the area on the counterattack and smashed the ball into the net in the 86th minute.
The defeat left Girona 18th in the 20-team standings on 37 points with one game left, three behind Celta Vigo who are just outside the relegation zone.
As Celta and Girona have an equal head-to-head record, the final relegation spot will be determined by goal difference, with Girona six goals worse off than Celta.
(Reporting by Richard Martin; editing by Tony Lawrence)
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