Lyubimets 2007, whose home town has a population of less than 8,000, stunned Ludogorets when midfielder Samir Aess took advantage of a defensive mix-up to score from close range in the 10th minute.
"It was an extremely poor performance by our team and it's inexplicable to me," said coach Ivaylo Petev, who has led Ludogorets to the title in the last two seasons. "You can't beat even a junior team when you're playing like this."
Ludogorets, who finished the game with 10 men after Romanian defender Cosmin Moti was sent off 18 minutes from time, host Slovan Bratislava in the return leg of their Champions League second qualifying round tie on Wednesday.
Slovakian champions Slovan won the first leg 2-1 after scoring twice in the last five minutes.
CSKA Sofia were held to a goalless draw against Lokomotiv Plovdiv at home as Stoycho Mladenov began his fourth coaching stint at the Sofia-based club, who signed nine new players earlier this week.
Bulgaria's top division was cut to 14 teams this season in a bid to improve standards.