The England striker marked the 10th anniversary of his debut Premier League goal with a double but that came after he helped the Potters take an 11th minute lead when he headed Charlie Adam's free-kick past David de Gea under pressure from Ryan Shawcross.
Just over 15 minutes later, Rooney became the first United player to score at both ends in a league game since David Beckham in 2001 when he played a one-two with Robin van Persie before scoring from a similar position to the opener.
van Persie made it 2-1 on the stroke of half-time when he slotted home Antonio Valencia's cross with his trusty left foot before Danny Welbeck added a third a minute into the second half, heading home a Rooney cross.
Michael Kightly got one back for Stoke just before the hour-mark when he advanced down the middle before unleashing an effort past de Gea after the ball bobbled off Rio Ferdinand but United were not done yet as Rooney notched up his 200th club goal by easily finishing van Persie's low cross from close range.
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