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Fans fought inside the stadium and crowd disorder delayed the Lyon-Besiktas kick-off by 45 minutes in the Europa League quarter-finals.
Incidents inside Lyon's stadium - which hosts the final next season - followed earlier clashes between French and Turkish fans on the streets.
Borussia Dortmund players return home
Head coach Thomas Tuchel says his players are still in emotional shock after their bus was targeted by a bomb attack on Wednesday.
Elsewhere, Manchester United stayed on course to complete its full set of European trophies by drawing at Anderlecht 1-1 in their first-leg game.
Henrikh Mkhitaryan scored in the first half and the Belgian side levelled in the 86th to add intrigue to the return match at Old Trafford next Thursday.
Ajax captain Davy Klaassen scored twice in a 2-0 win over visiting Schalke, whose goalkeeper Ralf Faehrmann stopped a rout.
Celta Vigo beat Genk 3-2 after trailing early then scoring three first-half goals.
After a delayed kickoff in Lyon, Besiktas led at halftime through Ryan Babel's low shot in the 15th minute. Lyon waited until almost time to score twice in two minutes.
Both clubs will be fined by UEFA, which increased security measures at all Champions League and Europa League matches this week after Borussia Dortmund's team bus was targeted by a bomb attack on Tuesday (Wednesday AEST).
The disorder in Lyon spread about 20 minutes before the scheduled kick-off.
French fans spilled on to the field for their own safety as fireworks were set off and missiles thrown from an upper section of the stadium housing Besiktas supporters.
Lyon president Jean-Michel Aulas was among the officials on the pitch trying to restore calm.
Besiktas likely faces the heavier sanctions from UEFA, which can close sections of the Turkish champion's stadium at the return match in Istanbul next Thursday (Friday AEST).
A brilliant late header by Leander Dendoncker earned Anderlecht a 1-1 draw against Manchester United.
Manchester United took an away lead through Henrikh Mkhitaryan, the Armenian firing home from a tight angle after Marcus Rashford's effort was repelled.
But Ivan Obradovic crossed for Dendoncker who crashed a header home in the 86th minute.
AP