The Group I game, with no away fans permitted, was interrupted when a flag depicting so-called Greater Albania, an area covering all parts of the Balkans where ethnic Albanians live, was flown over the terraces and pitch by what appeared to be a remote controlled mini drone near the end of the first half.
A Serbian player eventually grabbed the flag at the Partizan stadium, prompting an angry reaction from Albanian players and an unsightly melee ensued.
Riot police then moved in when around a dozen fans invaded the pitch and attacked the Albanian players, forcing them to retreat into the tunnel as flares were thrown from the terraces.
After a delay of around half an hour, English referee Martin Atkinson abandoned the game, which stood at 0-0.
"What happened is something we can't comprehend at the moment," Serbia captain Branislav Ivanovic said.
"On behalf of my team, all I can say is that we wanted to carry on and that we shielded the Albanian players every step of the way to the tunnel (after the riot broke out),” he added.
"The Albanian team said they were unfit physically and mentally to carry on after talking to the officials and they will now decide the fate of this match. We can only regret that football took a back seat but it is difficult to draw any conclusions or make any comments now,” he further said.
Albanian captain Lorik Cana told Albanian television: "I saw my players being attacked and hit even inside the tunnel, and even by the stewards. We were not in the right psychological or physical state to continue playing."

Serbian state television reported that Olsi Rama, the brother of Albanian Prime Minister Edi Rama, was arrested in the VIP section on suspicion of instigating the flag stunt.
Albanian Interior Minister Saimir Tahiri said that to the best of his knowledge Olsi Rama had left the stadium for the airport, according to information he had from Serbia's interior ministry and Albanian officials in Belgrade.
Asked if he had been arrested on suspicion of organising the drone stunt, Tahiri said: "Not to my knowledge. It's speculation."
Security was tight for a game at which no away fans were present and held against a backdrop of long-running Serb-Albanian tensions over Kosovo, a majority-Albanian former Serbian province that declared independence in 2008.
NATO waged a 78-day air war in 1999 to halt the killing and expulsion of ethnic Albanians in Kosovo by Serbian forces fighting a two-year counter-insurgency war. Serbia does not recognise Kosovo as independent.
Serbian Foreign Minister Ivica Dacic was quoted on the website of a Serbian daily as saying: "This was a political provocation.”
"The main question for me is how will the European Union and UEFA react, because if someone from Serbia had unveiled a flag of Greater Serbia in Tirana or Pristina (capital of Kosovo) it would already be on the agenda of the UN Security Council,” he said.
UEFA match delegate Harry Been said: "It is a regretful situation on which we will report; the referee, myself and the security advisor. The circumstances were such that we couldn't continue the match.”
"You all saw what happened and I cannot comment on who is to blame or what to blame. I will submit a report with my colleagues to UEFA and UEFA will decide what will happen further,” he added.

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