Ferguson started van Persie and Rooney together for the first time in Tuesday's Group H clash in Romania and the United manager was delighted to see his two star forwards strike up an immediate understanding.
With Rooney mostly dropping deep or wide while van Persie roamed alongside Mexican striker Javier Hernandez, United had too much firepower for the Romanian champions.
Cluj had taken a shock lead when Pantelis Kapetanos punished sloppy defending from Patrice Evra and Jonny Evans to drive a low shot past David De Gea in the 14th minute.
But United were able to maintain their 100 percent start to the competition thanks to van Persie and Rooney.
Ferguson's side equalised when van Persie looped Rooney's free-kick into the net off his shoulder and the Dutch forward bagged the winner four minutes into the second half with a clever flick from Rooney's lofted pass.
The duo's combination play drew praise from Ferguson, who expects van Persie and Rooney to fire his side's challenge to regain the Premier League and Champions League titles.
"The best quality both of them have is that they can turn a game," said Ferguson.
"That is an important feature. It doesn't really matter if they have a personal combination, it is their ability to finish moves off.
"We have a pair of really top players who can finish and change a game.
"The second goal was fantastic. It was a great ball from Wayne.
"I thought he had hit it too far in front of Robin. But the speed to get to the ball and his deftness of touch were fantastic."
Rather than use the duo in an orthodox front two, Ferguson slotted Rooney into a position just ahead of midfield and the Scot made it clear he intends to keep opponents guessing with his use of the pair.
"There is always going to be an issue because everyone expects it to be a miracle combination," he said.
"The strength of our team now is definitely in the forward positions.
"We have good alternatives, with Wayne, Shinji (Kagawa), Van Persie, (Danny) Welbeck and (Javier) Hernandez."
Ferguson also revealed that Northern Ireland defender Jonny Evans, who was replaced by Scott Wootton in the latter stages, is likely to be available for Sunday's trip to Newcastle.
"It is a dead leg," Ferguson added. "He got injured on Saturday and had a recurrence of that. He has five days to recover for Sunday. Hopefully he will be OK."
After a lacklustre display against Spurs on Saturday, van Persie was back to his predatory best and his double took his United goal tally to seven in seven starts since his £25 million move from Arsenal in August.
Van Persie is happy enough with his finishing, but he is keen to display his creative side as well.
"I think I am on the way to settling in well, but I would like to make more assists," van Persie said.
"It is not only about goals but I want to make more assists. I would like to improve that. I am on a good run but I would like to do better."
Ferguson will be delighted to hear van Persie isn't resting on his laurels, but the Dutch star shouldn't need to worry about providing too many assists if Rooney continues to play with such maturity.
"Everything starts with a good pass, so I have to thank Wayne for that. Not many players can make a pass like that," van Persie said when asked about his second goal.
"When it came to him I knew he could see that pass and give it the way I wanted it.
"I think it is the first time we have started together, we were both really pleased with that. We did it together."