The United striker informed the Scot of his viewpoint shortly after he had handed in a transfer request, having questioned the club's ambition in the process.
However, Ferguson has revealed that he told Rooney that it was "none of his business" who the club signed.
"My response was to ask Wayne: 'when have we not challenged for the league in the last 20 years?' How many European finals have we been to in the last three or four years?," he wrote in his autobiography. "I told him that to say we weren't ambitious was nonsense.
"Wayne said that we should have pursued Mesut Ozil, who had joined Real Madrid from Werder Bremen. My reply was that it was none of his business who we should have gone for.
"I told him it was his job to play and perform. My job was to pick the correct teams. And so far I had been getting it right."
Ozil went on to join Arsenal in a deal worth £42.5m in August this year.