United spared Brugge no mercy as Louis van Gaal enjoyed the joint-biggest win of his time as United boss.
Rooney will come up against more formidable defences than Brugge’s this year, but his goals will do his confidence no harm as he now seeks to get back to scoring ways in the Premier League.
The 29-year-old latched on to Memphis Depay’s through-ball to put United ahead in the 20th minute before converting passes from Ander Herrera and Juan Mata to record his first hat-trick since September 2011.
Herrera completed the rout in the 63rd minute after Brugge’s defence went to pieces – and it would have been five had Javier Hernandez not missed a late spot-kick.
With the fear of dropping into the Europa League running through their veins, United started nervously.
Herrera, making his first start of the season, looked the most tense player on the pitch, giving the ball away frequently and entering the book for a foul on Victor Vazquez.
Only a last-ditch block from Luke Shaw stopped Tom De Sutter from giving Brugge an early lead before Boli Bolingoli-Mbombo burst through a static defence but backheeled to no one despite having a chance to shoot on goal.
Brugge paid for their profligacy when Rooney broke the deadlock in the 20th minute.
Just as they did in the first leg, the Brugge defence allowed Depay to cut in from the right flank. He strode past three players and slipped the ball through to Rooney, who nudged the ball past Brugge goalkeeper Sinan Bolat.
Brugge cranked up the pressure before the break. Sergio Romero saved awkwardly from De Sutter and flapped at another shot before redeeming himself on the stroke of half-time by diving at Abdoulay Diaby’s feet to pinch the ball off the dallying striker.
Van Gaal replaced Adnan Januzaj with Bastian Schweinsteiger at half-time and pushed Herrera into the number 10 position.
Within four minutes of the restart, the former Athletic Bilbao man had supplied Rooney with his second as he drifted out to the right flank to pick up Depay’s pass before squaring to Rooney, who tapped in the easiest of finishes.
The skipper rounded off his hat-trick in the 57th minute. This time it was Mata who supplied a low pass from the right which Rooney converted.
Rooney could have scored his fourth moments later when he broke through the Brugge defence but chipped the ball wide.
Herrera did not pass on the chance to add to the scoresheet just before the hour, though. The midfielder raced on to Schweinsteiger’s through-ball and stroked the ball past Bolat to seal United’s place in Thursday’s group stage draw.
United could have added a fifth when Rooney’s cross struck Duarte’s hand and the referee pointed to the spot. The skipper selflessly handed the ball to Hernandez, but he slipped and put the spot-kick wide.