It has been claimed Isabel suffered minor injuries in the collision which occurred at 3am in Hollywood, Los Angeles.
Shia - who suffered injuries to his head and knee and required "extensive surgery" to his hand - was arrested and charged with driving under the influence (DUI).
However, Isabel's agent Theresa Peters has refused to confirm her client was present at the crash.
She said: "Everything out there is complete speculation and gossip. She's at work today. She's back on the set of 'Transformers 2'."
Before the accident, Shia was allegedly seen drinking shots of alcohol at a nightclub in the city.
A source told Us Weekly magazine: "He was dancing around and acting really crazy. He kept doing shots of whiskey. He stayed until the band was done and then stumbled out of the club."
Meanwhile, the actor has spoken about his troubled relationship with alcohol.
In an interview for the September edition of Details magazine, Shia said: "It's not something that is conducive to being a role model. And I don't know how to do it like a gentleman. I don't know how to have one drink."
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