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Ferguson's sides have long been renowned for mounting improbable late comebacks, but it looked like the tables were about to be turned at the Etihad Stadium on Sunday when Pablo Zabaleta netted an 86th-minute equaliser for City.
The Argentine's low drive made it 2-2 after Yaya Toure had chipped away at the two-goal advantage given to the visitors by Rooney's first-half brace, but an injury-time free-kick by Robin van Persie ensured United came out on top.
United's win, which also represented City's first league defeat of the season, gives Ferguson's team a six-point lead over their derby rivals after 16 matches of the campaign.
Although the manner of victory was dramatic, Rooney says that such late flurries are so deeply embedded in his club's DNA that they cannot be considered accidental.
"There is desire and passion at the club, and under Sir Alex we never know we're beaten," said Rooney.
"It's no fluke how many games we've won late on. We know it could be in injury time or in the first minute. You've got to keep on pushing."
Victory was especially satisfactory for United in the context of last season's encounters with City, which saw Roberto Mancini's men win 6-1 and 1-0 en route to their first league title in 44 years.
"It's a great day for us, to go six points clear and beat our greatest rivals, especially after what happened last year," added Rooney.
"We've waited a long time for this to happen. We know how much it means to everybody at the club, all the fans, and we're delighted.
"We're going to celebrate. They've had a great record here and to spoil that is a great feeling."
Rooney opened the scoring in the 16th minute with a delicate shot that left his England colleague Joe Hart stranded in the City goal, before doubling his tally in the 29th minute by converting a low right-wing centre from Rafael.
The second goal was the 27-year-old's 150th strike in the Premier League, making him the youngest player to reach that milestone, while he is also now United's all-time leading goal-scorer in derby matches with 10 goals.
