Rooney suffered a hairline fracture of his left foot in an accidental clash with Duberry during Sunday's Premier League draw at Old Trafford and will be out for two months.
"It was a complete accident," Duberry told Reading's official website.
"I hope and wish him all the best and the most speedy of recoveries - not just for Manchester United's sake but for England's too."
Duberry is mindful of Rooney's previous injury problems - as well as his own - and is hoping the striker is fit again as soon as possible.
As well as speaking out publicly, Duberry has been in touch with United defender Ferdinand to relay his best wishes to Rooney.
"He has already been through the trauma of injury, and I know myself what it is like," he said.
"To be hurt in the first game of the season is even more disappointing, and now he is facing the long haul of rehabilitation."