The result at the Georgi Asparuhov stadium gave new Levski coach Nikolay Mitov a dream start a day after he replaced Ilian Iliev.
But the game was marred by three red cards and controversial decisions by referee Stefan Spasov, who dismissed Levski's Slovenian midfielder Rene Mihelic as well as Lokomotiv's Brazilian midfielder Tom and his team mate Alexander Branekov.
In an unprecedented move, the Bulgarian Football Union's referees' commission took Spasov off the referees' list for an unspecified period for "extremely poor refereeing" only two hours after the end of the match.
Levski, chasing their 27th league title, top the standings with 49 points from 22 matches, followed by Ludogorets, who meet Lokomotiv Plovdiv on Monday, on 48.
Botev Plovdiv thrashed Pirin Gotse Delchev 5-0 to move up to third with 44 points.
Guinea-Bissau striker Basile de Carvalho opened the scoring after 18 minutes, converting a penalty after being brought down by Lokomotiv defender Alexander Dyulgerov.
Lokomotiv substitute Krum Bibishkov equalised in the 59th minute and Levski's Portuguese substitute Joao Silva hit the target with a precise shot from the edge of the penalty area 12 minutes from time to make it 2-1.
Tom was dimissed for a second bookable offence midway through the first half, Mihelic was red-carded for elbowing Dimitar Iliev in the 6th minute, and Branekov was also shown a straight red, for a challenge on Levski substitute Antonio Vutov 17 minutes from time.
Lokomotiv president Nikolay Gigov criticised the referee. "Such people should not be part of Bulgarian football," he told reporters. "This referee should be out."
- Sports & Recreation
- Bulgarian Football Union
- Lokomotiv Plovdiv