After a week of rumors, JustJared.com is reporting that Rosie Huntington-Whitely has been cast as Megan Fox's replacement in Transformers 3. This wouldn't be the first time she has worked with Transformers 3 director Michael Bay as he has directed her in Victoria's Secret commercials. Their source says "Rosie started training for the Transformers role already. She’s working hard."
It remains unknown exactly how much screen time she will have since the script is being adjusted to account for the change in circumstances and character. Training does indicate she will be involved in stunt work which indicates at least a supporting role much like Sam's parents but potentially larger. It also explains why she was added to the movies' insurance policy. Thanks to Brian for the link.
Update: Still nothing official from Paramount but Access Hollywood is now also confirming the story. Considering their tight relationship with the studios, this is nearly official confirmation.