The striker was recovering from a broken metatarsal in the runup to the tournament in Germany, with Ferguson claiming that his injury was too severe for him to be included in Eriksson's England squad.
However, the Swede has confirmed in his new autobiography that he picked Rooney based on medical advice from the Three Lions physio, a decision that infuriated Ferguson.
Eriksson wrote: "Leif [Sward, England doctor] and I met Ferguson and United's doctor at the United training ground. 'He cannot play in the World Cup', Ferguson said flatly. The doctor brought out some X-rays that he said showed Rooney's broken bone would not heal in time.
"When the doctor finished, Leif looked him in the eye. 'Why do you sit here and lie to me?' Leif asked. "He was one of Europe's foremost specialists on this kind of injury.
"I just wish I could have filmed Ferguson's face when Leif explained that Wayne's break would heal in time for the World Cup. When Leif had finished, I turned to Ferguson. 'Sorry, Alex,' I said. 'I will pick Rooney'."
Rooney failed to score at the tournament and was sent off for stamping on Ricardo Carvalho in the quarter-final clash with Portugal that England lost on penalties.