As the playoffs for Europe's elite club competition reached their climax, Bayer Leverkusen, BATE Borisov, CSKA Moscow and Astana joined United in securing the final places in Thursday's draw for the lucrative group stage.
Astana became the first Kazakh team to qualify when they drew 1-1 at APOEL Nicosia for a 2-1 aggregate success and Leverkusen thumped visiting 10-man Lazio 3-0 on the night to go through 3-1.
BATE of Belarus lost 2-1 at Partizan Belgrade but advanced on away goals after the tie ended 2-2, while CSKA Moscow eliminated Sporting Lisbon 4-3 on aggregate.
Rooney, who had not scored in almost 900 minutes before United's trip to Belgium, netted his first goal of the season and his 30th in the Champions League in the 20th minute.
Running on to a neat Memphis Depay pass into the penalty area, the England international clipped the ball over onrushing goalkeeper Sinan Bolat.
It was Depay's second assist of the tie and he also netted a double in last week's 3-1 first-leg success.
Depay was again involved in the buildup to Rooney's second four minutes after halftime.
The Netherlands forward found Ander Herrera in the penalty area, whose first-time pass across goal set up Rooney for a simple tap-in.
Herrera's Spanish compatriot Juan Mata provided the assist for Rooney's third eight minutes later, as he completed his first treble in Europe since his debut against Fenerbahce in 2004.
Herrera made it 4-0 in the 63rd minute when he collected a Bastian Schweinsteiger pass and slotted home before Javier Hernandez missed from the penalty spot nine minutes from time.
After failing to qualify for last season's competition for the first time since the 1995-96 season, United are through for the 20th time, equalling the record shared by holders Barcelona, 11-times winners Real Madrid and 2004 champions Porto.
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 holders Barcelona, Real Madrid, 2014 finalists Atletico Madrid and Sevilla, who qualified as last season's Europa League winners.
Malmo, Dinamo Zagreb, Maccabi Tel Aviv and Shakhtar Donetsk also won their playoff ties on Tuesday.
