David Moyes' side beat the Greek champions 3-0 at Old Trafford to progress to the Champions League quarter-finals with an aggregate 3-2 lead, having lost the first leg 2-0 in Greece.
It was Van Persie who got the goals for Moyes' men, scoring a hat-trick and naturally attracting all the attention for a brilliant display.
But statistically, Rooney had a better overall game, despite not finding the back of the net.
For starters, the 28-year-old completed six successful dribbles, the highest tally of any United player. Rooney's nearest rival in this respect was Danny Welbeck, who also enjoyed a night to remember against Olympiakos.
Of Man United's attacking trio, though, Rooney again impressed by making the most passes, while the England man was also one of just three United players to play a through ball during the game.
Crosses were another an area of promise, with Rooney attempting six of them - the highest total of any United player once again. Here, though, the 28-year-old was admittedly trumped, as he didn't make a single accurate cross, while Van Persie and Ryan Giggs both made two.
But perhaps the most encouraging stat of all was the amount of tackles the striker won last night. With Moyes' side having kept a clean sheet and generally impressing defensively, how on earth did Rooney end up making the most tackles of anyone on the field?
It appears that that is just how Wayne Rooney operates. With five successful challenges, the Man United man made one more tackle than Rafael, two more than Phil Jones - and at least three more than everyone else in a red shirt.
While Van Persie will walk away with all the credit for United's win, then, Rooney was every bit as vital to United's overall display. He didn't leave Old Trafford with three goals last night but, in many ways, the 28-year-old offered a lot more than the ability to simply put the ball in the back of the net.