Ferguson left Rooney on the bench for the 3-2 victory over Fulham, where the Englishman suffered a deep gash after coming on as a substitute.
With Rooney now sidelined for around four weeks, the duo cannot be partnered yet but Ferguson is convinced they will gel together.
When asked if they could forge a formidable partnership, the Scot replied: "Yes absolutely. There's no doubt about that. And (Danny) Welbeck can play with them, there is no question about that. I have good options. That is where it is going to be difficult."
"Van Persie is flexible because he can play in different positions, from the right, in behind the strikers. He is such a mobile player, there are great options with him. And Wayne can play behind and he can play up. [Javier Hernandez] is the only one-position player and that is through the middle."
United play their third match of the Premier League season at Southampton this afternoon.