The provocative map showed Albania's borders expanded to include parts of four neighboring countries: Serbia, Macedonia, Montenegro, and Greece.
CAS has also docked Serbia three points, ordered the team to play the next two games in front of an empty stadium, and pay a fine of EUR 100,000.
The Lausanne court thus rejected Serbia's appeal, and accepted that filed by Albania, "because it found no evidence that Albanians refused to resume the match," while its considers the interruption to have occurred "due to the bad organization of the game and the violent invasion of the pitch of fans who attacked the guests."
The Albanian team was fined EUR 100,000 "for responsibility for the drone released during the game that carried a flag with nationalist and patriotic symbols."
Reacting to the news on Friday, Albanian Prime Minister Edi Rama - whose brother the authorities in Belgrade initially suspected of being behind the drone incident - posted on Twitter, "Supeeeer! This is European justice! Three points for red-and-blacks in Belgrade!!!"
Serbian Prime Minister Aleksandar Vucic responded with two tweets in which he decried "European justice turning into global injustice for the umpteenth time," and also said that "those who caused the incident have been rewarded, while the victim has been punished."
"Lausanne Court decision is an embarrassment for justice, judiciary and an insult to all normal people," according to Vucic's tweet.
The CAS decision should now be registered by UEFA, whose disciplinary commission in October awarded Serbia a 3-0 victory in the canceled qualifier, docking the team at the same time three points.