The Group I contest in Belgrade - which was set against a backdrop of political tensions - was abandoned following a disturbance that prompted violent scenes involving players and spectators.
Towards the end of the first half, with the game scoreless, a drone carrying a flag featuring Albanian national symbols entered the stadium and hovered over the pitch.
The two sets of players clashed after Serbia defender Stefan Mitrovic attempted to pull the flag down, and a number of supporters then invaded the pitch as the situation escalated.
Albania's players were pelted with missiles as they left the field and the fixture was duly abandoned, with both teams unable to agree on a resumption.
In a statement on Wednesday, UEFA confirmed Albania will be investigated for "refusing to play" and "the display of an illicit banner".
Serbia, meanwhile, are facing an array of charges, with European football's governing body set to deal with the case on October 23.
"Disciplinary proceedings have been opened against the Football Association of Serbia [FSS] for the setting off/throwing of fireworks and missiles, crowd disturbance, field invasion by supporters, insufficient organisation and use of a laser pointer," read UEFA's statement.
"Proceedings have also been opened against the Football Association of Albania [FShF] for refusing to play and the display of an illicit banner.
"The case will be dealt with by the UEFA Control, Ethics and Disciplinary Body on 23 October."
Earlier on Wednesday, the Serbian Football Association issued a strongly-worded statement condemning the appearance of the drone and Albania's apparent refusal to resume the fixture after referee Martin Atkinson had initially led the teams from the field.
"They [Albania] simply took UEFA rules in their own hands interpreting them as they preferred," claimed the FSS.
"According to that, we estimate that they are directly guilty for the match abandonment and we expect that UEFA disciplinary bodies will register the match with 3:0 result, in favour of Serbia."
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