Slavia’s 1-0 win at home to Ferencváros failed to overturn a two-goal deficit from the first leg.
United States forward Jordan Siebatcheu scored twice in the first half to rally Switzerland's Young Boys to a 3-1 win, and 4-2 on aggregate, after conceding early against Cluj.
Former European champions Benfica and PSV Eindhoven will meet in the playoffs in a rematch of the 1988 final after both advanced 4-0 on aggregate against Spartak Moscow and Midtjylland, respectively.
Ludogorets Razgrad, the champion of Bulgaria, beat Olympiakos in a penalty shootout after the teams were tied 3-3 on aggregate. Ludogorets benefited from the abolition of the away-goals rule this season, which would previously have sent Olympiakos through after the 2-2 second-leg draw.
Shakhtar Donetsk won 2-1 in each leg against Genk to earn a playoff against Monaco, the 2004 Champions League beaten finalist. Monaco coasted past Sparta Prague 3-1 at home Tuesday and 5-1 on aggregate.
The Czech Republic and Scotland have seen both its team eliminated before the playoff round that is played over the next two midweeks.
The 32-team group-stage draw will be made Aug. 26 in Istanbul. (AP)