Spanish side Malaga secured a place in the group stage of the Champions League for the first time in their history after holding out for a 0-0 draw at Panathinaikos.
Leading 2-0 from the first leg of the play-off, thanks to goals from Martin Demichelis and Eliseu, Manuel Pellegrini's side produced a solid defensive display in Athens.
Malaga are facing uncertainty behind the scenes amid speculation that their Qatari owner is looking to sell up. Spain midfielder Santi Cazorla and Venezuela striker Salomon Rondon have already been sold to Arsenal and Rubin Kazan respectively.
Braga booked their place in the group stages after coming through a penalty shoot-out against Udinese.
After a 1-1 result in the first leg in Portugal, 90 minutes could not separate the teams at the Stadio Friuli as Pablo Armero's 25th-minute header for the hosts was cancelled out by another header, from Ruben Micael, in the 72nd-minute.
Extra-time produced no more goals and so the contest went to penalties, with Braga winning 5-4.
Anderlecht, who were demoted to the third qualifying round after Chelsea's Champions League title last season forced UEFA to reshuffle the places, left it late before sealing a 3-2 aggregate success against Cypriots AEL.
The Belgians lost the first leg 2-1 and were going out heading into the last nine minutes of the return match - until goals from Dieumerci Mbokani and Oleksandr Yakovenko gave them a 2-0 win.
An early goal by Portuguese midfielder Tonel gave Dinamo Zagreb, Croatian champions for the last six seasons, a 1-0 win at Maribor in neighbouring Slovenia and sent them through 3-1 on aggregate.
It was a bad night all in all for the visitors, who had Soares Arghus sent-off five minutes from time.
BATE Borisov joined Dinamo in the group stage following a 1-1 draw (3-1 aggregate) at Israeli champions Hapoel Kiryat Shmona.
Laszlo Lencse's free-kick gave the Israeli side hope with a goal midway through the second half but their hopes of progress were snuffed out by Aleksandr Pavlov's equaliser four minutes into injury time.