The Portugal international saw his effort with the outside of his boot diverted into the back of the net off Nat Phillips with the Premier League officially awarding the goal to the United man.
It took his tally for the season to 28.
No Premier League midfielder had previously scored more goals than Frank Lampard did in the 2009-10 season for Chelsea, finding the back of the net 27 times as the Blues celebrated a Premier League and FA Cup double.
Bruno moves ahead however having also scored one less penalty than Lampard did that season, with nine to his name.
Yaya Toure sits in third place having scored 24 times during the 2013-14 season.
Fernandes has now been directly involved in 44 goals in 50 Premier League appearances for United with 26 goals and 18 assists.
Only Eric Cantona and Robin van Persie have been involved in more goals in their first 50 league appearance with 46 and 45 respectively.
United’s early goal got them off to a bright start but goals from Diogo Jota and Roberto Firmino saw Liverpool head into half-time in the lead.
Liverpool added a third early in the second-half with Firmino on the score sheet again.
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