The 71-year-old controversially left the England striker out of his starting lineup against Real Madrid which fueled speculation that he could be sold in the summer.
However, Sir Alex has dismissed the speculation as "rubbish" and insists there is no issue between him and his striker.
He snapped at reporters: "The Wayne Rooney nonsense first? Or do you want to talk sense? The issue you're all going on about is rubbish. There's absolutely no issue between Wayne Rooney and I."
He continued to explain, "The suggestion we don't talk on the training ground is nonsense. The decision to not play him was purely tactical and he understood that. Wayne will be here next year, you have my word on that."
Sir Alex also revealed that he expects the 27-year-old to play a part in Sunday's FA Cup clash with Chelsea.