The Group I game erupted into controversy shortly before half-time in Belgrade when the banner attached to the drone, apparently flown in by remote control from fans outside the stadium, was brought down by Serbia defender Stefan Mitrovic.
That seemed to upset a number of Albania players, several of whom attempted to intercept the black banner, which contained the Albanian flag in the centre.
It prompted a melee involving numerous players and forced English referee Martin Atkinson to lead the teams off the field, after some disruption off the pitch as well.
There were no signs of play being restarted more than half an hour after the suspension, with UEFA then confirming the match had been abandoned.
UEFA match delegate Hari Bin confirmed the governing body will investigate what transpired.
Quoted by Serbian media, including the popular Sportske website, he said: “You saw what happened and at this point I cannot speculate further as to who was responsible and accountable. UEFA will take further steps on the basis of the official report.”
Albanian supporters had been banned from entering the stadium by UEFA on safety grounds and the match was set against a backdrop of tight security.
Tensions have never been far from the surface between the nations over Kosovo, the province with which both countries share a disputed border and is recognised as independent by the United States and major European Union countries but not by Serbia.
The tie was goalless at the time of the suspension and clear-cut chances were in short supply in the Serbian capital.
Zoran Tosic and Branislav Ivanovic both missed the target from the edge of the area as the hosts attempted to force the issue while Dusan Tadic’s long-distance effort was well blocked by Albania defender Andi Lila.
The best chance of the game fell to the visitors as an Ansi Agolli free-kick from the left wing found Mergim Mavraj, whose shot from inside the area was tipped wide by Serbia goalkeeper Vladimir Stojkovic.
From the following corner, Lorik Cana’s header at the far post sailed wide, while the visitors were appearing to gain the upper hand when a drone was flown into the stadium.
There seemed to be no immediate threat to the match, with numerous players taking a drinks break as the drone flew harmlessly over the pitch.
However, that changed when Mitrovic attempted to bring down the banner that was attached to the drone, which infuriated some of the Albania players.
Following a skirmish, the situation appeared to escalate as the Albanian players were reportedly the target when objects were thrown on to the pitch, which led to Atkinson leading the players down the tunnel.