The verified @TwitterUK account took a swipe at the much-maligned Jones on Tuesday, posting: “Name a better footballer than Phil Jones”.
The incident came after the social media network had previously said “being the target of online abuse is not easy to deal with” on a dedicated help centre page about coping and reporting abuse.
United are understood to have complained to Twitter about the subsequently deleted post, with the social network apologising to both club and player.
Jones has endured a difficult season and missed out on a place in United’s squad for the current Europa League campaign with an ankle injury.
He last featured for Ole Gunnar Solskjaer’s team in January’s FA Cup fourth round win at Tranmere, netting the fourth goal in a 6-0 romp.
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