The 27-year-old scored twice to put Sir Alex Ferguson's men ahead 2-0, before goals from Yaya Toure and Pablo Zabaleta put the three points in doubt, with Robin van Persie winning the game with a free kick in the dying moments of the match.
The prolific forward leapfrogged the Red Devils' club legend to gain the derby record and is now level with Manchester City's Francis Lee and Joe Hayes with the overall record of 10.
The striker also became the sixth player to reach the 150 Premier League goals barrier, following in the footsteps of Alan Shearer, Andy Cole, Robbie Fowler, Thierry Henry and Frank Lampard in achieving the career landmark.
"I didn't know I was the top United derby scorer but I am proud of that," Rooney told reporters. "It is a great feeling to score against City. There is a lot of passion and pride in Manchester in these games and it has been great for me to score so many."
The former Everton forward was also glad to see the his strike partner's late effort hit the back of net, and he didn't begrudge Van Persie taking the free kick ahead of himself.
"I practice free kicks most days with Robin, Ryan Giggs and Ashley Young," Rooney said. "He is a fantastic striker of the ball. Before he took it I went over and asked him was he crossing or shooting, so I knew whether to get across my man or leave him space to shoot. He told me was shooting and thankfully it went into the bottom corner."