Swiss champions Young Boys returned to the competition following a 1-0 win away to Galatasaray that clinched a 4-2 aggregate victory.
Alan Virginius scored the only goal in the 87th minute in Turkey and Galatasaray goalkeeper Fernando Muslera was sent off for kicking out at the Young Boys substitute as he celebrated.
Salzburg are set for their sixth straight appearance in the main phase after a 1-1 draw at home to Dynamo Kyiv wrapped up the tie 3-1 on aggregate.
Adam Daghim struck early for Salzburg before Vladyslav Vanat equalised for the Ukrainians.
Salzburg will be one of two Austrian sides in Thursday's draw, joining Sturm Graz.
Sparta Prague also made it through qualifying as a 2-0 win over Swedish side Malmo completed a 4-0 overall triumph for the Czech champions.
Both teams missed a penalty in the return leg before Sparta netted twice late on courtesy of Lukas Haraslin's spot-kick and a goal from Albion Rrahmani.
The four remaining spots will be filled on Wednesday.
