The striker, who is now captain of the Red Devils, had reportedly threatened to leave three times during Ferguson's time in charge at Old Trafford.
Five years ago, Rooney signed a new deal thought to be worth around £200,000 a week, but prior to that, Ferguson decided to contact the owners to state that it would be unfair for the player to earn more money than his boss.
In his new book Leading, Ferguson wrote: "When the Glazers and David Gill agreed to a big increase in Wayne Rooney's salary in 2010, they wanted to know how I felt.
"I told them I did not think it fair that Rooney should earn twice what I made and Joel Glazer immediately said, 'I totally agree with you, but what should we do?'
"It was simple. We just agreed that no player should be paid more than me."