Borislav Mihailov has resigned from his role as Bulgarian Football Union president in the wake of the scandal that has engulfed the national team following their 6-0 defeat to England.
Play had to be stopped twice in the first half owing to racist chants coming from the home terraces during the Euro 2020 qualifier.
The first break prompted an appeal over the stadium's public address system urging fans to refrain from racist behaviour, in line with UEFA protocols.
Several spectators left the stadium during a second, more prolonged, stoppage shortly before half-time.
A statement released by the FA read: "Today the Bulgarian FA president Borislav Mihailov has resigned from his position – his letter of resignation will be presented to the members of the FA’s Executive Committee at this Friday’s meeting.
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"After many years spent in the post and with his many contacts at a high international level, Mr. Mihailov expresses his firm readiness to continue helping in the development of Bulgarian football in every possible way."
Earlier on Tuesday, Mihailov faced calls from the country's Prime Minister to step down from his post.
In a statement Boyko Borisov said: "I urge Borislav Mihailov to immediately resign as president of the Bulgarian Football Union!
"After yesterday's shameful loss of the Bulgarian national team and in view of the poor results of our football, I ordered the minister [of youth and sports] Krasen Kralev to terminate any relations with the Bulgarian Football Union, including financial ones, until Borislav Mihailov's resignation.
"I also strongly condemn the behaviour of some of those present at the stadium.
"It is unacceptable that Bulgaria, which is one of the most tolerant countries in the world, and [where] people of different ethnicities and religions live in peace, [is] associated with racism and xenophobia."
Bulgaria, who were already playing in a partially closed stadium as a consequence of UEFA sanctions, find themselves at the foot of Euro 2020 qualifying Group A with just three points, having failed to win any of their seven qualifiers to date.
They will attempt to end a 12-match winless streak, dating back to October 2018, when they play their final qualifier at home against the Czech Republic on November 11.