Braga qualified for the lucrative Champions League group stages after a memorable victory over Sevilla on Tuesday night, while Werder Bremen required a late goal and extra-time to see off Sampdoria.
Lima netted a hat-trick as Braga won 4-3 in Spain to progress 5-3 on aggregate. Portuguese side Braga held a 1-0 lead following the first leg and goals from Matheus after 31 minutes and Lima after 58 minutes, three minutes after he came on as a substitute, put the visitors 3-0 up on aggregate.
Luis Fabiano pulled a goal back after 60 minutes and Jesus Navas pulled Sevilla level on the night after 84 minutes. However, one minute later Lima netted his second before he added his third, leaving Frederic Kanoute's stoppage-time strike in vain as Sevilla fell into the Europa League.
Sampdoria had to overturn a 3-1 deficit from the first leg in Germany and raced into a 3-0 lead on home turf, but a late goal from Markus Rosenberg and an extra-time strike from Claudio Pizarro saw Bremen qualify.
Giampaolo Pazzini struck twice inside the first 13 minutes, the second a tremendous effort, while Antonio Cassano added a third. But Rosenberg struck in injury time, setting the stage for Pizarro to be the hero.
Partizan Belgrade defeated Anderlecht 3-2 on penalties in dramatic circumstances in Belgium. After a 2-2 draw on the night, loose turf around the penalty spot saw the home side send three of their penalties high over the bar.
Partizan took a 2-0 lead on the night thanks to two goals from Cleo but Anderlecht responded through Romelu Lukaku and Guillame Gillett before suffering spot-kick heartache.
Matias Suarez spooned the ball over the bar as the pitch appeared to give way around the penalty spot, but Mladen Krstajic missed Partizan's next spot kick.
Lucas Biglia also shot over for Anderlecht and Aleksandar Davidov missed for Partizan before the hosts' Mbark Boussoufa also fired over in the game's decisive miss.
Basle won 3-0 in Moldova to complete a 4-0 aggregate success over FC Sheriff. Marco Streller scored after 74 minutes and Alexander Frei netted twice in the final six minutes to seal victory.
FC Sheriff finished the game with ten men after captain Vazha Tarkhnishvili was sent off for two bookable offences after 76 minutes.
Erin Zahavi scored in the 92nd minute as Hapoel Tel-Aviv claimed a 4-3 aggregate success over Salzburg, who had taken the lead through Douglas da Silva's own goal three minutes before the break. The second leg ended 1-1.