Slovenia striker Roman Bezjak scored the winner 13 minutes after the break with his 20th goal in all competitions this season, giving Polish keeper Adam Stachowiak no chance with a right-foot drive after the defence failed to clear a corner.
The game was interrupted for more than 17 minutes soon after Bezjak's goal when Botev fans threw flares on to the pitch and a fire truck had to be quickly deployed to douse the flames.
Botev finished the game in the Black Sea town of Burgas with 10 men after their Brazilian substitute Vander Vieira was shown a red card late on for fouling winger Mihail Alexandrov.
"It's a pity that such a big football game was marred by all these troubles in the second half," Ludogorets's co-owner Georgi Domuschiev told reporters.
The hard-fought win at the Lazur Stadium underlined Ludogorets's dominance of Bulgarian football since 2011 when they were reached the top flight for the first time.
Ludogorets, based in the town of Razgrad with a population of less than 35,000, have won three successive league titles, two national cups and a domestic Supercup in three years.
The Eagles have played 63 matches in a marathon season that began in mid-July and included a 16-game Europa League campaign in which Stoycho Stoev's side reached the last 16.
"It's a dream season," said a delighted Stoev. "I hope we'll be able to do well in the Champions League next season."
Botev supporters destroyed part of the perimeter fence and more than a dozen of them invaded the pitch a few minutes before the final whistle as the fire truck was used again to quell more flares while the Ludogorets players came under attack.
The result meant twice Bulgarian champions Botev, one of the most popular clubs in the Balkan country, are stil waiting for their first silverware since they won the Bulgarian Cup in 1981.
- Sports & Recreation
- Adam Stachowiak
- Roman Bezjak