The third qualifying round first-leg tie against the Albanians was abandoned after Legia’s Slovakian midfielder Ondrej Duda appeared to be struck on the head by a stone thrown from the stands.
Duda was stretchered off for treatment and the remaining players followed him off the pitch with Legia leading 2-1.
Kukes were ordered to play their next two European home games behind closed doors and were fined 70,000 euros for setting off fireworks and throwing objects, as well displaying an illicit banner.
The second leg will go ahead as planned this Thursday.
Last year Legia Warsaw were thrown out of the Champions League for fielding an ineligible player during the final few minutes of their qualifier against Celtic, which they won 6-1 on aggregate.
Meanwhile, UEFA has thrown out a protest by Fenerbahce after they complained their Champions League opponents Shakhtar Donetsk had fielded midfielder Fred in last week’s tie despite allegations of a doping offence against the Brazilian.
Shakhtar coach Mircea Lucescu selected Fred for the third qualifying round first leg in Istanbul, which ended 0-0, while admitting the club had been advised by UEFA not to include him.
On Friday, the Brazilian Football Confederation confirmed that Fred had tested positive for the masking agent hydrochlorothiazide during the Copa America in Chile.
However, a spokesman for UEFA said: “The protest has been dismissed.”