Argentine forward Matias Tissera was on target from close range five minutes after the break, scoring his 12th league goal of the season from Bulgaria captain Kiril Despodov's corner.
The Razgrad-based side, who will enter next season’s Champions League qualifying rounds, finished on 85 points, one point ahead of CSKA, who beat Levski Sofia 2-0 but remain without a title since 2008.
Ludogorets ended the game at the Black Sea city of Varna with 10 men after Portuguese midfielder Claude Goncalves was sent off in the dying minutes but it did not dent the celebrations at the club, who have been on a roll since the return of former coach Ivaylo Petev in March to replace Slovenian Ante Simundza.
"It was more difficult this time," said Petev. "We had many difficult games but I think we deserve the 12th title."
The season-long title duel between Ludogorets and CSKA Sofia came down to the final day but the holders knew a win would make it safe.
The win also completed their third domestic double having beaten CSKA 1948 3-1 in the Cup final.
CSKA beat city rivals Levski in a tense affair thanks to goals from Norwegian midfielder Tobias Heintz and Haiti striker Duckens Nazon but it was all too late.
CSKA blew their chance of ending their 15-year wait for the title after drawing 1-1 at home against CSKA 1948 last weekend, when captain Ivan Turitsov missed a penalty awarded following a VAR intervention in the 12th minute of added time.
Ludogorets are the fifth European team to claim at least 12 straight titles after Latvia's Skonto Riga, Gibraltar's Lincoln Red Imps (both 14), Norway's Rosenborg and BATE Borisov of Belarus (both 13).
Bayern Munich won their 11th successive Bundesliga title last month - a record for the big five leagues.