Rooney, a first-half replacement for Michael Owen, powered a header past Brad Friedel with 16 minutes to go as United claimed their fourth League Cup final success.
Villa had taken the lead early on through a James Milner penalty but Owen levelled for United before hobbling off through a hamstring injury.
But, after a decent spell of Villa pressure, Sir Alex Ferguson's men took the lead with yet another Rooney header.
Antonio Valencia and Berbatov played a neat one-two down the right, the former's cross picked out Rooney 12 yards from goal and he strained his neck muscles to send a majestic header into the top corner.
Villa piled bodies forward in search of an equaliser but United held out to make it back-to-back Carling Cup wins.