Ludogorets thrashed Montana thanks to an early goal by Bulgaria midfielder Svetoslav Dyakov and a second-half double from substitute Mihail Alexandrov while Levski, who started with a two-point lead, were held 1-1 at home by city rivals Slavia.
Levski's title hopes were ended by defender Dimitar Vezalov 16 minutes from time when he put the ball into his own net from seven metres with no Slavia player around him after Basile de Carvalho had lifted the home side with a first-half strike.
Ludogorets finished with 72 points from 30 matches ahead of Levski on 71 with CSKA Sofia third on 63.
A few minutes after the final whistle, Levski's chief executive Ivo Tonev said he would resign while the club's financial director Konstantin Bazhdekov collapsed with suspected heat stroke and was rushed to hospital.
Ludogorets and Levski both had a chance to clinch the title on the last day of the season but the Razgrad-based club profited from their rivals' misfortune to become champions, an outcome considered "unthinkable" by the Bulgarian media.
Levski had seemed certain to win a 27th league title when their Guinea Bissau striker De Carvalho capitalised on a defensive mix-up to put them in front after 33 minutes.
But Slavia equalised against the run of play when Vezalov scored one of the strangest own goals of the season after a right-wing cross by Slavia's Japanese midfielder Daisuke Matsui.
Levski had won their previous seven league matches, including a last-gasp victory against Ludogorets, but were unable to find a winner, leaving their supporters at the Georgi Asprauhov stadium in a state of shocked silence.
"I don't feel well, we should have scored two or three goals," said Levski coach Nikolay Mitov. "It's a huge disappointment, it hurts, it's painful."
The Eagles, as Ludogorets are known in the Balkan country, are based in a town of less than 35,000 people, but clinched their maiden championship in a domestic treble last season.
"I don't want to underestimate last year's title but this one is so sweet," said Ludogorets coach Ivaylo Petev, whose side who have lost only twice in the league this term. "We're one level above our rivals."
"Last season, we also won the title on the last day of the season, it happened again and I hope we'll win it next year too," added Petev.
Ludogorets, who were in the third division three years ago, sealed a place in next season's Champions League second qualifying round, while Levski go into the Europa League first qualifying round along with third-placed CSKA.
Four-times Bulgarian champions Lokomotiv Sofia, who have played in the top division for the last 61 seasons, escaped relegation with a 2-1 win over CSKA on Saturday.
Bulgaria's top flight will be cut by two teams to 14 next season as the domestic governing football union (BFU) tries to improve standards.