"Based on the official reports and the current available evidence at the disposal of the Uefa disciplinary bodies, the control, ethics and disciplinary body (CEDB) has considered that the supporters of both clubs were responsible for the crowd disturbances at the match," said a Uefa statement.
The teams play the second leg of the quarter-final on Thursday night in Istanbul with Lyon leading 2-1.
The Lyon president, Jean-Michel Aulas, described the sanction as fair and added. "We will see if we appeal. But we respect the decision of Uefa. We had some responsibility," he wrote on the club's website.
However, the Turkish champions were furious with the ruling. Besiktas blamed the Lyon police force for the disturbances which forced a 45 minute delay to the start of the first leg.
"There is nothing to say about this scandalous decision," Besiktas press spokesman Metin Albayrak told NTV television. "It shows how biased a decision Uefa has made by putting us on an equal level with Lyon over incidents we were not responsible for," he added. "Lyon's police should be held entirely responsible for the incidents that broke out."
Hundreds of supporters were involved in scuffles outside the Parc OL before the match and police used teargas to quell outbreaks of fighting and vandalism. Lyon supporters then poured onto the pitch as they attempted to protect themselves from firecrackers and other objects raining down from the stands above the pitch.