Luuk De Jong claimed an 109th-minute winner as PSV Eindhoven edged Monaco 3-2 in extra-time, to go through 4-3 on aggregate.
Benfica beat Midtjylland 3-1 to win 7-2 on aggregate thanks largely to midfielder Enzo Fernandez and 20-year-old striker Henrique Araujo who scored before Pione Sisto responded for the Danes.
In Scotland Malik Tillman completed a turn around when he scored the decider with 11 minutes left as Rangers beat Union Saint-Gilloise 3-0.
The Belgian outfit had won the first leg 2-0 in their first appearance in European competition since 1964-65.
Kostiantyn Vivcharenko and Viktor Tsygankov guided Dynamo Kiyv past Austrians Sturm Graz 3-1 over two ties with efforts in extra time.
Earlier, Moldovans Sheriff Tiraspol, were knocked out by Viktoria Plzen as the Czech outfit won 4-2 over two legs.
The first leg of the play-offs take place on August 16/17 with the return fixtures a week later.