Manchester derby: Robin Van Persie breaches City's fortress
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City issued a statement apologising to Ferdinand while the FA also confirmed they will investigate the incident which could have repercussions for the home club.
Ferguson, however, preferred to revel in the positives of his side's performance which again displayed their ability to outscore opponents even when creaking at the back.
"You couldn't take your eyes off it today, it was so engrossing. It tells you about the quality of the Premier League, it's such a great league," Ferguson, whose side have scored 40 goals and conceded 23 in 16 games, said.
Rooney put United ahead after a 16th-minute counter-attack ended with him scuffing a low shot into the corner.
It was not the sweetest connection but meant the 27-year-old became the youngest player to reach 150 Premier League goals, a feat only managed by Thierry Henry, Alan Shearer, Robbie Fowler, Andy Cole and Frank Lampard.
Rooney made it 2-0 in the 29th minute with a cool finish after fine link-up play between Rafael and Antonio Valencia.
It was clinical by United while City, who had also lost centre back and captain Vincent Kompany to injury, appeared deflated.
Mancini lost patience with striker Mario Balotelli seven minutes into the second half, replacing the disgruntled Italian with former United striker Carlos Tevez.
With Balotelli stewing in the dressing room, the game suddenly changed in the space of a minute on the hour.
First Ashley Young was wrongly judged offside as he slotted into an empty net after Van Persie's shot hit the woodwork.
City, instead of being 3-0 down, immediately went down the other end where Tevez showed great composure to set up Toure to fire past David De Gea who had twice made stunning blocks.
Belief flooded back into the City ranks and Zabaleta's thumping finish made it 2-2 in the 86th minute and even raised home hopes of an unlikely victory.