Bogomil Marinov said he had filed a police complaint after Stoichkov phoned him three days after the tense league match.
"He called me on Tuesday night, introduced himself and began to insult and threaten me," Marinov told the Association of Bulgarian football referees' website on Friday. "He told me that it had been my last match as a referee."
Marinov, who said he now planned to give up refereeing professional games, sent off Litex striker Marcelo Nicasio early in the second half after the Brazilian made minimal contact with Slavia defender Daniel Zlatkov.
Nicasio, who has scored six goals since joining Litex in January, had received a yellow card for shirt-pulling while celebrating his goal in the first half.
Nicasio missed Litex's match at Beroe Stara Zagora on Wednesday after the Bulgarian Football Union (BFU) rejected an appeal from the club.
The champions were held to a 1-1 draw after five straight victories and are fifth in the standings with 38 points, seven behind leaders Ludogorets.
Marinov, 34, said: "I have decided to quit professional refereeing but I love football so much and I can't imagine my life without football.
"I'll continue in amateur football though I know the pay difference is huge."
Former Barcelona striker Stoichkov, known for his aggressive manner in his playing days, declined to comment.
"I will not comment on such groundless accusations," Stoichkov, 46, said in a statement. "I will only say that since returning to Bulgaria to take charge of Litex, I'm showing much more tolerance toward referees than when I was a footballer."
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