Monkey chants and apparent Nazi salutes during Monday's match in Sofia caused indignation in the football world and led to the resignation of Bulgaria's football federation chief.
The Bulgarian Football Union (BFU), however, said in a statement https://bfunion.bg/news/46463/0 Balakov had resigned due to the team's recent run of unsatisfactory performances and that the executive committee had accepted it.
"We did what we had to do regarding the security during the game versus England".
They conclude their qualifying campaign at home to Czech Republic on November 17.
It was twice halted in an effort to stop the racist abuse.
He later issued a statement making a "sincere apology" to the England team and anyone else offended by the racist abuse. "Together with Kick It Out, the English Football League, The FA and the PFA, it has a vital role to play in promoting equality across the country".
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Immediately after the match Balakov refused to accept that England players were subject of such abuse, but later backtracked and apologised to the opposition.
Twelve arrests were made following the game with Bulgarian authorities having identified 16 suspects.
British Prime Minister Boris Johnson and his Bulgarian counterpart Boyko Borisov alike condemned the incident.
An 18-year-old man was charged with "grave hooliganism," while four other soccer fans were fined and received two-year bans from sporting events.
Mihaylov resigned later on Tuesday, but the BFU's first vice-president Yordan Letchkov would not accept Mihaylov's initial resignation over fears of political interference.
UEFA has opened disciplinary procedures against both Bulgaria and England for their fans' behaviour during the game. The five others were handed fines and banned from soccer matches.