Nine-man Rangers crashed out to Swedish side Malmo 2-1 on aggregate, after an ill-tempted clash at the Swedback Stadium. The Scottish champions lost Steven Whittaker to a red card after 19 minutes, but managed to level the tie soon after with a goal from Nikica Jelavic.
Madjid Bougherra was the second Rangers player sent off on 66 minutes, before Malmo lost Ricardinho for a second bookable offence. The Swedish side ultimately prevailed courtesy of Jiloan Hamad's 80th-minute equaliser.
Russian side Rubin Kazan progressed to the Champions League play-off round with a 4-1 aggregate victory over Dynamo Kiev of Ukraine.
Rubin took a 2-0 lead into the home leg of the tie, where goals from Vladimir Dyadyun and substitute Igor Lebedenko made for a comfortable evening. Oleh Gusav grabbed a consolation for Dynamo.
Dutch side FC Twente are also safely through. A 0-0 draw in Romania against FC Vaslui made sure of their progress, 2-0 on aggregate.
Apoel FC won 2-0 away to Slovakian champions Slovan Bratislava to go through by the same score on aggregate. Ailton put the visitors ahead just before the hour mark, before Bratislava were reduced to 10 men when Erik Grendel picked up a second booking in the space of 12 minutes.
Gustavo Meduca sealed Apoel's progress, the Italian midfielder making it 2-0 on the night deep into injury time.
Czech Republic champions FC Viktoria Plzen survived a scare against Rosenborg of Norway to continue forward progress in their debut Champions League campaign, winning 3-2 on the night and 4-2 on aggregate.
Plzen took a 1-0 lead into the home leg, but saw it cancelled out by a Mikael Lustig goal on the stroke of half-time. They hit back quickly through Marek Bakos and Daniel Kola, but when Rade Prica replied to make it 3-2 on aggregate he looked to have set up a tense finale. But almost immediately Milan Petrzela made sure of Plzen's famous victory.
FC Zurich of Switzerland beat 10-man Standard Liege 1-0 at home, to advance 2-1 on aggregate.
Liege lost Yoni Buyens to a straight red card on 21 minutes, and their Champions League hopes were killed off by Admir Mehmedi's winner just before the hour mark.
Wisla Krakow will be joining them in the pot for the play-off round draw on Friday. The Polish champions wrapped up a 5-2 aggregate win against Litex of Bulgaria with a 3-1 home victory.
Midfielder Maor Melikson helped himself to a brace on the night, with substitute Cezary Wilk grabbing the third late on. Nikolay Bodurov got Litex's consolation.
Sturm Graz are also safely through. The Austrians beat FC Zestafoni of Georgia 1-0 at home to achieve a 2-1 aggregate win. Striker Roman Kienast made the decisive contribution, scoring the winner on 68 minutes.
Israeli champions Maccabi Haifa overcame the challenge of NK Maribor. Maccabi managed a 1-1 draw in the second leg in Slovenia, prevailing 3-2 on aggregate.
Idan Vered put the visitors ahead in the 10th minute, before Maribus captain Markus equalised shortly after the half-hour mark.
Dinamo Zagreb made sure of their progress with a 3-1 aggregate victory against HJK Helsinki of Finland. The Croatian champions won the away leg 2-1, and it looked like things would stay that way until the final moments of the home return. With 90 minutes on the clock Argentine defender Luis Ibanez grabbed the winner on the night.
Belgian side KRC Genk earned a spot in the play-off round with a hard-fought 3-2 aggregate win against FK Partizan of Serbia.
Nemanja Tomic's 40th minute opener for Genk made it 2-2 on aggregate and had the Belgians going through on away goals. But Jelle Vossen equalised from the penalty spot on 58 minutes and the visitors held on.
Two-time European Cup winners Benfica could only draw 1-1 away at Trabzonspor AS in Turkey, but the Portuguese champions advanced 3-1 on aggregate to book a spot in Friday's draw.
Spanish midfielder Nolito put Benfica ahead on 19 minutes, before Paulo Henrique equalised just after the half-hour mark. Trabzonspor were reduced to 10 men when Adrian Mierzejewski was shown a straight red on 58 minutes, however, and there their challenge ended.