Referee Tasko Taskov and his assistants Tsvetan Trifonov and Valentin Dobrev have been stood down with immediate effect after BFU president Borislav Mihaylov personally demanded the sanction.
"It is high time referees learnt to be responsible for their decisions, on and off the pitch," UEFA Executive Committee member Mihaylov said after an emergency meeting with refereeing commission chief Nikola Dzhuganski.
Botev, who slumped to sixth place after the defeat, appealed against the refereeing, saying the officials influenced the outcome of the game.
The twice Bulgarian champions said Taskov wrongly disallowed a goal scored by Botev striker Ivan Tsvetkov and failed to award a penalty when Ludogorets's Ivory Coast winger Franck Guela handled the ball in the penalty area.
"I'm disappointed with the refereeing in the match, to say the least," said Dzhuganski, who is set to give a special news conference on Friday.
Angry Botev fans flooded online forums with insults while Taskov's obituary was posted on a club Facebook account.
Ludogorets, who are based in Razgrad, a town with a population of less than 35,000, were playing in Bulgaria's third division two and a half years ago, but clinched a maiden league title and domestic treble last season.
They currently top the standings with 35 points from 14 games, but many clubs have complained that they receive favourable treatment from referees and no penalty has been awarded against them in their last 52 games.
- Sports & Recreation
- Borislav Mihaylov