"The bruise is very unique and is consistent with blunt-force trauma. Something struck the tongue," said Dr. Louis Pena.
Pena also testified that there were bruises on Clarkson's right arm and wrist.
Pena called Clarkson's death a homicide, and he described the actress as a hopeful person with no history of depression or suicide attempts.
Spector, 67, is accused of shooting Clarkson, 40, in February 2003 after she agreed to accompany him to his mansion from her job as a hostess at the House of Blues on the Sunset Strip.
The defense claims that Clarkson committed suicide by placing the gun in her own mouth and pulling the trigger.
Photos: The Phil Spector Trial
Pena said there was no evidence that Clarkson had been putting her affairs in order in advance of a suicide. The coroner said Clarkson had been taking two drugs generally given for depression, but her neurologist had prescribed them for her chronic headaches.
"I found her to be a hopeful person from the notes I read," Pena said.
He said she died with a purse on one shoulder in a stranger's home, which is not typical of someone taking her own life.
Jurors were shown graphic photos of the damage done to Clarkson's face and the inside of her mouth.
At least one juror looked away from the large display on a movie screen, and for the first time, Clarkson's mother and sister were not present in the courtroom.
Pena said the recoil from the shot shattered Clarkson's top front teeth, blowing them out of her mouth. He said that the shot went through her head, severed her spine and death would have been almost instantaneous.
Several women have testified about their relationships with Spector and violent encounters with him that involved threats with a gun.
Spector rose to fame in the 1960s with what became known as the "Wall of Sound" recording technique that changed pop music. Clarkson was best known for her role in Roger Corman's 1985 cult film "Barbarian Queen."