The 31-year-old bent the set-piece into the top corner to notch a 250th United goal.
It means he is now the club's all-time leading scorer outright having equalled Sir Bobby Charlton's tally of 249 earlier this month.
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Mark Hughes was fuming at the decision to add five minutes of stoppage time
And Hughes, who played for United earlier in his career, believes Rooney's record won't ever be broken.
"It is an outstanding record and won't be surpassed," he told the BBC.
"It has taken 40-odd years for Sir Bobby's record to be broken which shows how high a mark it was."
Hughes also criticised the five minutes stoppage time that was added on at the end.
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Wayne Rooney prevented Stoke from securing all three points
Rooney equals Bobby Charlton's record with historic goal
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"I didn't feel there was five minutes added on but that gave them enough time to get something out of the game," the Welshman added.
"We are disappointed but we need to pick ourselves up.
"We were within seconds of beating a very good Manchester United team."