It was a strange day for Rooney though, who also became the first United player to score at both ends in a league game since David Beckham in 2001.
In fact, it was an odd afternoon all told given the own goal meant United once again had to come from behind, recovering courtesy of Rooney, Robin van Persie and Danny Welbeck, only to require Rooney's second to ease nerves created by a Michael Kightly goal for the visitors in Saturday's Premier League clash at Old Trafford.
And the thrills will only partially divert attention away from Rio Ferdinand's decision to snub Sir Alex Ferguson by refusing to wear the Kick It Out anti-racism T-shirts worn by all his outfield team-mates in the pre-match warm-up.
Ferguson said on Friday he felt Jason Roberts was misguided in his determination not to wear the shirts, so Ferdinand's reasoning will be interesting, even if his position is somewhat easier to understand given the year-long dispute between brother Anton and former England team-mate John Terry.
Away from the politics, Ferguson had described Stoke as the "jolly green giants" prior to the game.
Yet it was Tony Pulis' side who looked like they had the magic beans, such was the gusto with which they attacked their hosts.
Charlie Adam in particular was a major threat, providing Stoke with the kind of direct midfield momentum United so obviously lacked.
It was the Scot's touchline free-kick that Rooney ended up nudging into his own net.
In a packed six-yard box, under pressure from Ryan Shawcross and facing his own net, Rooney was in an impossible situation once Adam had drilled the ball beyond the near-post.
It was not the way Rooney would have wanted to score for the first time this season, and condemned United to conceding the opening goal for an incredible seven occasions out of 11 games in all competitions.
And the damage was nearly much worse as Adam chanced his luck from the opposite touchline, forcing David de Gea into a fine reaction save as the United defence was almost caught out.
Ferguson has spoken optimistically of United's defence becoming more secure once there is consistency in selection.
It does not seem to be happening though, despite Ferdinand and Evans playing alongside each other in central defence for the fifth time on the trot, with the exception of a Capital One Cup tie.
However, if defending remains a chore, United are thrill-a-minute heading the other way.
Danny Welbeck, twice, and Patrice Evra both wasted glorious opportunities before Van Persie and Rooney linked up to drag the hosts level.
Rooney fed his strike partner to the left before heading off into the box, where an inch-perfect cross was delivered.
From a similar position to the one he found himself in at the other end, Rooney again found the net.
Stoke continued to forage but United were now on one of those familiar rolls, and the visitors had no way of halting the steamroller.
Welbeck should have put his side in front from Rooney's cross, then clipped the crossbar with a curling effort.
But when Van Persie stole into space to meet Antonio Valencia's cross, the deft-close range finish rolled into the corner.
A minute after the break, United had another. Rooney was the provider this time with a cross that invited Welbeck's flying header.
Jonny Evans was denied a fourth by Asmir Begovic's magnificent save and Welbeck was inches away from turning home Rafael's cross as he slid in at the far post.
Nothing is secure for this United team, though.
Kightly's charge straight down the centre of the pitch has been seen far too often for comfort, and after a fortunate ricochet off Ferdinand, the midfielder calmly finished.
It was the seventh goal the Old Trafford outfit had conceded on home soil in four league games this season, a quite startling statistic considering they have kept a clean sheet in that run.
Rooney was destined to end a hero, though.
Twenty-seven on Wednesday, the Merseysider was captain fantastic for England in San Marino, hooked and humbled in Poland.
On Saturday, he completed his double century of club goals for United and Everton in the easiest manner possible as Van Persie's low cross bobbed about in the six-yard area before rolling to the far post, where an unmarked Rooney tucked home.
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