The first leg tie last week in Lyon had been marred by angry clashes between fans that resulted in a delay to the start of the game and led to both sides receiving bans - suspended for two years - from their next European competition.
Having won the opening leg 2-1 last week - a victory overshadowed by a lengthy delay due to crowd disturbances, which led to both clubs being charged by UEFA and facing a potential suspension from competition in the future - Lyon were beaten by the same scoreline before keeping their cool in a penalty shootout at the Vodafone Arena on Thursday.
A disciplinary statement read regarding Lyon's punishment: "The charges against the French club were related to crowd disturbances, setting off of fireworks, stairways blocked, insufficient organization and field invasion by supporters after their second goal".
"What is important is to salute the Lyon team who, despite all the adversities of the last 10 days, have succeeded in an incredible story", said Lyon president Jean-Michel Aulas.More news: Philip Morris International Profit Advances 4% In Q1
"The decision taken by UEFA regarding the match played in Lyon can not be justified and accepted by our club", a statement said. "We had some responsibility", he said on the club website.
In the other quarter-final tie, Lyon defeated Besiktas on penalties after the two legs ended 3-3 on aggregate. "We will follow the process by making the necessary objections to UEFA".
"Lyon's police should be held entirely responsible for the incidents that broke out". There were a number of firecrackers that exploded over our fans' heads so they had only one option, to flee onto the pitch.
Up to 20,000 Turkish fans, the majority living in France or Germany, were intermingled among the 35,000 supporters of Lyon on top of the 3,000 fans from Istanbul situated in the visitors' section. "There is no need to punish Besiktas", club spokesman Metin Albayrak told state-run Anadolu news agency before the UEFA ruling on Wednesday.More news: Former NFL player Aaron Hernandez hangs self in MA prison cell
The second leg of the quarter-final tie takes place in Istanbul on Thursday and comes after Lyon were involved in another ugly flashpoint over the weekend.
The Besiktas fans were in fine voice but were nearly silenced early on when Corentin Tolisso broke into the box and controlled Lacazette's pass but could only fire wide.
Besiktas and Lyon played out an extraordinary game in Istanbul that could comfortably have had eight or nine goals each.More news: First Family attends their first Easter Egg roll
- Malcolm Mitchell: 'Almost brought me to tears' to be mentioned by president
- US Republican vows 'all hands on deck' in Georgia congressional runoff
- UK Foreign Secretary Cancels Moscow Visit
- The GKN plc (GKN) Rating Reiterated by Liberum Capital
- New test results indicate use of sarin gas in Syria
- EPA to reconsider oil and gas industry emissions requirements
- UN strongly condemns North Korean missile launch after delay
- Lynn may play for KKR again this season: Kallis
- Aaron Hernandez's family to donate his brain for CTE research
- Food and Farm-Milk Dispute story