having won the first leg 1-0.
Igor Stasevich put BATE ahead after 25 minutes after the ball bounced into his path, only for Partizan to level after 74 minutes via an own goal from BATE’s Maksim Zhavnerchik.
An injury-time Ivan Saponjic goal proved academic in the end as Partizan earned a hollow victory on the night.
2010 quarter-finalists CSKA Moscow also advanced after a come-from-behind 3-1 success against Sporting Lisbon — 4-3 on aggregate — to add to their record of seven wins out of seven in Russia this season.
Portuguese giants Sporting had taken a 2-1 advantage to Moscow and Teofilo Gutierrez scored an away goal after 36 minutes before a second half double from CSKA’s Ivorian striker Seydou Doumbia on 49 and 72 minutes left the tie level.
Nigerian striker Ahmed Musa got the winner for the Russians five minutes from time as they qualify for the main draw for the third straight season.
On a superb night for Louis Van Gaal’s Manchester United in Belgium, Dutch midfielder Memphis Depay had a role in Rooney’s first two goals on 20 and 49 minutes, with a Juan Mata cross eight minutes later allowing the United captain complete his hat-trick.
Spaniard Ander Herrera compounded a night of misery for the Belgian club after 63 minutes following a Bastian Schweinsteiger cross to put the three-time winners of the Champions League through in style, despite substitute Javier Hernandez missing a late penalty.
Manchester United — winners in 1968, 1999 and 2008 — didn’t feature in the competition last season but had previously reached the group stages for 18 years in succession.
Brugge have not made the group stages since the 2005/06 season and coach Michel Preud’homme admitted the outcome was logical.
“It’s a top team and they are top players. They have everything,” said Preud’homme of the English club.
“We are there to learn something and I hope we can learn a lot from these two confrontations.”