Benfica wrapped up top spot in Group C of the Champions League with a 1-0 win over Romanian minnows Otelul Galati at the Stadium of Light. Oscar Cardozo's seventh-minute goal was enough to seal the Portuguese side's victory.
Napoli took until the 65th minute to score their opener against Villarreal, who finished without a point from their six group games. Gokhan Inler scored the first and Marek Hamsik made it 2-0 late on.
In a remarkable turnaround in Group D, Lyon joined group winners Real Madrid in the knockout stages after Bafetimbi Gomis scored four goals in a 7-1 win over Dinamo Zagreb in Croatia.
Lyon had started the night with only a faint hope of qualification as they had to hope Real beat Ajax and that they won in Zagreb with a shift of at least seven goals in their favour.
The Dutch side's 3-0 home loss to Real, who finished the group with a 100% record, was only to be expected with two strikes from Jose Callejon sandwiching an effort from Gonzalo Higuain.
If things did not already look bleak for Lyon they got even worse away to Dinamo Zagreb when Mateo Kovacic put the home side ahead on 40 minutes despite, Jerko Leko's early sending-off.
But Lyon responded in emphatic style with Gomis equalising just before half-time and adding three more of his own in the second half, along with strikes from Maxime Gonalons, Lisandro Lopez and Jimmy Briand, to secure qualification.
There were more dramatic scenes in Group B where CSKA Moscow snatched a 2-1 win away to group winners Inter Milan, leapfrogging Trabzonspor and Lille to claim second place.
The Russian side's only hope was that their two group rivals played out a draw while they pulled off an improbable win at the San Siro.
Lille and Trabzonspor duly obliged with a cagey 0-0 draw in France. Seydou Doumbia gave CSKA hope with a 50th-minute opener but Esteban Cambiasso immediately cancelled that out. CSKA's crucial winner came three minutes from time through Vassili Berezoutski.