Rooney has been getting much criticism fans and pundits due to poor form as the England striker had gone 10 games without a goal for United prior to Wednesday.
The United skipper kept working hard and answered back to his critics in style when he hit a hat-trick in Belgium with Ander Herrera scoring the fourth goal.
Manchester United will discover their group opponents in today’s draw in Monaco having missed out on Champions League football last season.
“To go through to the group stage after being out of it last year is a great result. We look forward to the draw now tomorrow,” said Rooney.
“It was a big disappointment last year not to challenge in it. We didn’t think it would be as comfortable as it was, but it was vital we went through any way we could.
“Over the two legs we deserved that. We’ll enjoy the draw and it is nice to be back in there again.”
Club Brugge Coach Michel Preud’homme admitted the outcome was logical for his team having not reached the group stages since the 2005/06 season.
“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.”
Meanwhile in Germany Bayern Leverkusen smashed visiting 10-man Lazio 3-0 on the night to go through 3-1 on aggregate.
Lazio had gone in Germany defending their 1-0 goal advantage and reach the group stages for the first time since the 2007/08 season but Leverkusen proved too strong for them.
Leverkusen scored through Hakan Calhanoglu, Admir Mehmedie and Karim Bellarabi in a game which saw Lazio’s Brazilian defender Maurício being sent off for a second yellow card in the 70th minute.
In the other games, Astana became the first Kazakh team to qualify when they netted a late equaliser to draw 1-1 at APOEL Nicosia for a 2-1 aggregate. Serbian midfielder Nemanja Maksimovic snatched the crucial goal for Astana six minutes from time as Kazakhstan became the 32nd country to be represented in the group stage.
Spain are the first country to have five clubs in the group stage in one season after Valencia progressed past Monaco 4-3 on aggregate despite a 2-1 defeat at the Ligue 1 side in their playoff second leg on Tuesday.
Valencia joined Barca, Real Mdrid, Atletico Madrid and Sevilla, who qualified as last season’s Europa League winners.
Read more on uefa.com