Mondays clash in Sofia was marred by the racist abuse of England players, with the game stopped twice during the first half as officials threatened to abandon the match.
Bulgaria have been charged on four counts, those being racist behaviour - with UEFA noting the chants and Nazi salutes that were heard and seen during the game - throwing of objects, disruption of the national anthems, and for playing replays on the grounds screen.
England have likewise been charged with the disruption of the national anthems, as well as having an insufficient number of travelling stewards. The case will be dealt with by the UEFA Control, Ethics and Disciplinary Body, with the date of the meeting to be clarified in the future.
UEFA president Aleksander Ceferin released a statement earlier on Tuesday, saying: "There were times, not long ago, when the football family thought that the scourge of racism was a distant memory.
"The last couple of years have taught us that such thinking was, at best, complacent. The rise of nationalism across the continent has fuelled some unacceptable behaviour and some have taken it upon themselves to think that a football crowd is the right place to give voice to their appalling views."
He added: "Football associations themselves cannot solve this problem. Governments too need to do more in this area. Only by working together in the name of decency and honour will we make progress."
The president of the Bulgaria Football Union, Borislav Mihaylov, resigned on Tuesday after being told to quit by the nations prime minister, Boyko Borissov.
Monday nights events have been largely condemned by footballers, including a number of England players who were involved in the 6-0 victory. The win means the Three Lions can secure qualification for Euro 2020 at home against either Montenegro or Kosovo in November.