Stewards looked to be injured from the violence as police and medics tried to safely take them away from the violence.
According to Lyon's official Twitter account, projectiles and fireworks were also being launched in the stands.
They were dispersed by security guards and no arrests were made.
Authorities had labelled the fixture "high risk", with around 500 police reportedly stationed at the stadium - more than double the usual amount.
It was feared before the match that the game could be used for a political statement ahead of Sunday's Turkish referendum, which may increase the powers held by President Recep Tayyip Erdogan.
Aulas is seeking reassurances from UEFA over whether the second leg can still go ahead.
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Aulas told Lyon fans on April 10 to support the team "because there will be a strong opposition and many Turks inside the stadium", reports France 24. "& #8220;When you see how this fury spilled over on all sides we have become scared".
The distressing images from the Parc Olympique Lyonnais stadium follow hours of clashing among rival French and Turkish followers earlier in the city.
"The Lyon hooligans attacked children", said the Yeni Safal daily newspaper, with a picture it said showed a French fan waving a crutch in the direction of a child.
The Union of European Football Association (UEFA) will be fining both teams, but Besiktas will probably face heavier sanctions. Fans began to rush towards the field to escape, interrupting the players who had just taken the field for their warmups. There were a number of firecrackers that exploded over our fans' heads so they had only one option, to flee onto the pitch.
"I've heard some people ask 'but how could a pitch be invaded?'".
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