Braga, who beat Lech Poznan 2-0 for a 2-1 aggregate win, in the next round.
Serb Miralem Sulejmani scored two early goals as four-times European champions Ajax completed a 5-0 win over their Belgian opponents and former UEFA Cup winners Anderlecht.
The Portuguese will next play Paris St Germain after the French side went through on away goals against BATE Borisov.
Russian champions and 2008 UEFA Cup winners Zenit St Petersburg came back from the brink of elimination to beat Young Boys Berne 3-1 and 4-3 on aggregate.
Ammar Jemal gave the Swiss the lead in a game which kicked off in a temperature of minus 9 Celsius, slightly warmer than predicted earlier this week.
Spartak Moscow drew 1-1 at home to FC Basel in even colder conditions - around minus 15 - to go through 4-3 on aggregate and earn a tie against Ajax.
With CSKA Moscow qualifying on Wednesday for a last 16 tie with Porto, compatriots Rubin Kazan, who squandered a 2-0 lead at Twente Enschede to draw 2-2 and lose 4-2 on aggregate, were the only Russian side to go out.
Twente will play Zenit in the next round.