Serbia have been ordered to play their next two home games in Group I behind closed doors, while both teams have been fined 100,000 euros (USD 126,900), European football's governing body added.
Both sides said they had been treated unfairly and would appeal the decision.
The match, played on October 14 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 pitch by a remote-controlled drone.
Serbian player Stefan Mitrovic grabbed the flag at the Partizan stadium, prompting an angry reaction from the Albania team.
A brawl broke out after several Albanian players snatched the flag from Mitrovic and then had to run for cover into the tunnel as the invading home fans attacked them.
Riot police moved in when about 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.
The match was abandoned with the score at 0-0.

The Albanian federation (FHSF), rejecting the official charge of "refusing to play", said UEFA's ruling had overlooked the situation inside the stadium.
"There FHSF has no responsibility for the entrance of the drone and banner into the Partizan Stadium. Security is a liability of the organiser,” the ruling added.
"The FHSF cannot be responsible for lack of security in the Serbian territory inside and outside the stadium,” it said.
"There is clear medical evidence that Albania players were, physically and mentally, unable to play due to injuries stemming from the violence of the home supporters entering the pitch... The pitch remained unsafe,” the ruling further added.
"The Albanian players were never notified that the official had decided to resume the match,” it said.
The Serbian FA (FSS), officially charged by UEFA over the "the setting off/throwing of fireworks and missiles, crowd disturbance, field invasion by supporters, insufficient organisation and use of a laser pointer", also protested.
"We have the impression that the FSS is a constant target of newly-discovered punitive measures, for as far as we know it is an unprecedented measure to deduct points from a team who have at the same time been awarded a walkover win," said the FSS in a statement.
The game was 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.
The incident led to a diplomatic row between the countries and the prime ministers of Serbia and Albania agreed to postpone a meeting scheduled for Wednesday.
Albania's Edi Rama had been due to visit Belgrade on October 22 – the first such trip by an Albanian leader in 68 years that was widely seen as a chance to reset ties after a long history of tensions between the Balkan nations.
He will now make the journey on November 10 to allow tempers to cool.
Serbian officials have accused Rama's brother, Olsi Rama, of sparking the chaos by releasing a small drone trailing a nationalist Albanian flag over the match venue. He has denied the accusation.

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