Although racist chanting was heard from the stands and reported by England players, most of the Bulgaria players and their coach claimed after the match they had not heard any abuse of the visiting team.
Bulgaria’s football union president resigned on Tuesday, a day after racist abuse marred a match against England in Sofia.
"Today the president of the Bulgarian Football Union Borislav Mihaylov presented his resignation, which will be handed in to the members of the executive committee on its meeting on Friday," the union said in a statement on its website.
The decision "resulted from the tension created over the past days, which is detrimental to Bulgarian football and the Bulgarian football union," the statement said.
The Euro 2020 qualifier, which England won 6-0, was twice halted by racist chanting aimed at England players.
Earlier, Bulgaria’s prime minister called on Mihaylov to resign.
A group of black-clad Bulgarian fans, some of whom were making right-wing salutes, were moved from an area behind the dugout with home team captain Ivelin Popov trying to appeal to the supporters in a heated discussion at halftime.
"I urge Borislav Mihaylov to immediately resign as president of the Bulgarian Football Union!" Boyko Borissov posted on Facebook on Tuesday, after the footage of Monday night's match was seen around the world on TV and social media.
"It is unacceptable for Bulgaria, which is one of the most tolerant countries in the world, and people of different ethnicities and religions live in peace, to be associated with racism and xenophobia."
Earlier, Sports Minister Krasen Kralev said the government would suspend relations with the BFU, including financial ties. The Bulgarian Football Union (BFU) was not immediately available to comment.
However, after Monday's match, it tried to play down the incidents. "It's quite disappointing to focus on racism," BFU vice president, Yordan Lechkov, said.
"It's not serious to concentrate on that if there’s a qualifier like this and we're playing against a team like England."
UEFA had ordered the BFU to partially close the Vasil Levski national stadium for England’s visit after supporters were found guilty of racist behaviour in matches earlier this year.
Racist chanting was heard from the stands and reported by England players to manager Gareth Southgate, with the referee informed and a public announcement made on two occasions. Most of the Bulgaria players and their coach said after the match they had not heard any abuse of the visiting team.
Coach Krasimir Balakov said there had not been such racial incidents before and blamed England fans for being disrespectful to Bulgarian supporters.
"During the second half they used words against our fans which I find unacceptable," he said.
The BFU and a number of Bulgarian clubs have been fined for racist abuse several times over the past few years. Troy Townsend, of soccer equality campaign group Kick It Out, urged UEFA to ban Bulgaria.