Lyon also advanced, holding on to get through 5-4 on aggregate despite a 2-1 loss at Roma.
The French side carried a 4-2 lead into the Estadio Olimpico and an early goal from Mouctar Diakhaby gave the hosts an uphill climb.
Kevin Strootman struck back in the 17th minute and a Lucas Tousart own goal at the hour mark complicated the tie, but Lyon held on to reach the last eight of the competition.
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