Benfica completed a resounding 5-0 aggregate win over the Ukrainian runners-up with a 3-0 win in Lisbon after three first-half goals.
Nicolas Otamendi opened the scoring, before strikes from Rafa Silva and David Neres late in the half all but settled the tie.
Benfica reached last season’s Champions League quarter-finals.
Plzen reached the group stage for the fourth time in club history with a come-from-behind 2-1 win over Azerbaijani champions Qarabag.
Qarabag had taken a first-half lead after a goalless first leg, but Plzen responded with second-half goals from Jan Kopic and Jan Kliment to progress.
Maccabi secured their place in the group stage for a third time in dramatic circumstances against Red Star Belgrade.
After a 3-2 first leg win in Haifa, Maccabi trailed 2-0 with Aleksandar Pesic and Mirko Ivanic scoring in the first half.
But Maccabi pulled one back on half-time from Daniel Sundgren.
The game was headed for extra-time with scores locked 4-4 on aggregate until Milan Pavkov’s 90th minute own goal.