It made him the Red Devils' most prolific scorer in clashes against City, in addition to confirming him as only the sixth - and youngest - player to reach 150 Premier League goals.
But when Yaya Toure and Pablo Zabaleta turned the contest on its head, Ferguson admitted he would have been delighted with a point.
"You have to give credit to City," said the United boss. "They kept fighting and battling.
"They have this great record of scoring goals and when they got the second I thought, 'I will take the draw'."
Van Persie had other ideas, adding to his already impressive reputation by scoring his 14th goal of the season to ease United six points clear.
"It got a little deflection but it was a terrific hit," said Ferguson. "His whole game was fantastic. He has kept them on the back foot."
United's day would have been made easier had Ashley Young's goal been allowed to stand when he tucked home the rebound to a Van Persie shot which cannoned off the post.
Instead it was incorrectly ruled out for offside which, had the result not turned out the way it did, would surely have triggered a far less phlegmatic reaction from Ferguson.
"It was disappointing because from 3-0 up it went to 2-1 in minutes," said Ferguson. Football can kick you in the teeth but there will always be controversy in a match like that because there are so many things happening."
Ferguson believes United's advantage may be needed later in the season given City are now without European distractions.
He was pleased with his side's efforts though, the only downside coming with Jonny Evans' hamstring injury.
"He got it in the first half after a challenge with Mario Balotelli," said Ferguson.
"He played on but I always think while you can get through the first half, once you try to start the second after cooling down it is a problem.
Meanwhile, full-back Patrice Evra has rejected rumours of a move to Paris St-Germain in the summer.