Sheffield United were minutes away from securing a replay after Manchester United were awarded a late penalty.
Blades fans were left heartbroken when a Dean Hammond sliding challenge awarded the Premiership side a 93rd minute penalty.
Rooney slotted home to the dismay of the 8,500 travelling fans and sealed the Yorkshire sides fate.
The League one side managed to keep Manchester United at bayfor the majority of the game, with the Premiership side producing a lack-lustre performance.
Manager Louis Van Gaal admitted, “The result is okay and there is no escape, we won.
“The result was alright, but the performance was not alright.
“We moved the ball too slowly and with the defensive organisation they had, there were ten players behind the ball, then you have to make the pitch as big as possible. We didn’t do that in the first half.”
The Blades have a reputation as ‘giant killers’ having beaten Aston Villa, Southampton and West Ham in recent years and so would have fancied their chances against the Red Devils.
Perhaps Sheffield United’s undoing was the more defensive approach with the visitors producing only two shots on target.
However, the League One team will be disappointed with the result after a poor performance from their opposition.
On the match, Blades manager Nigel Adkins has said, ““A replay at Bramall Lane would have been fantastic for us…”
“But great credit to the players. We showed good character and a resilience, grit and determination – and discipline and concentration.
“We frustrated a very good Manchester United side and nullified the chances they had.
“We had 8,500 supporters today and I think they appreciated the effort and commitment of the players on show. You could see us as a football club really come together.”