Lisa Gavin, a forensic pathologist and medical examiner for Clark County, Nevada, was among the early witnesses on the second day of testimony.
Jurors were shown a photo of a green body bag at the beginning of her questioning, followed by a grisly photo of his body.
His relatives who remained in the courtroom looked away.
One woman got up to leave once the photos were shown.
The bullet entered Shakur's chest near his armpit, Gavin said, and travelled through his chest, including through a lung.
That caused his lung to collapse and bleed, and doctors ultimately removed the damaged lung in an effort to save his life, she said.
Additional bullets damaged his intestines and other parts of his body, she said.
Shakur died at a hospital six days after he was shot.
The images were not shown in the video feed from the trial.
Gavin was not at Shakur's autopsy but was called as an expert witness because the examiner from 30 years ago has since died.
As Gavin explained the autopsy photos, Davis sat still, looking at the screen in front of him.
He occasionally whispered in his lawyer's ear.
In Monday's opening statements, Deputy District Attorney Binu Palal told jurors that "Duane Davis did not pull the trigger. But he did plan the shooting in retaliation of the beating of his nephew," and that, "Remarkably, you will learn that from Duane Davis himself".
Davis, 63, could get life in prison if he is convicted of murder with a deadly weapon with the intent to promote, further or assist a criminal gang.
He has pleaded not guilty.
His lawyer in the defence opening called the prosecution's narrative "fiction".
Lawyer Michael Sanft told jurors Davis was not previously charged, despite implicating himself in interviews and his memoir, because law enforcement knew that he was "full of crap".
Jurors were shown video of Shakur's entourage attacking Davis' nephew Orlando "Baby Lane" Anderson outside the boxing match at the MGM Grand in Las Vegas hours before the shooting on September 7, 1996.
Davis spent the next two hours planning how to get even, said Palal, and Shakur was gunned down "in an act of revenge".
Palal told jurors Davis held onto a visceral hatred for Shakur for decades that drove him to speak repeatedly about it.
In a 2008 interview with federal investigators, he described handing a gun to the men in the backseat of a white Cadillac that fired on a black BMW with Shakur and Marion "Suge" Knight inside, Palal said.
In a 2009 interview with Las Vegas police, he admitted to his role in the killing, he continued.
He further implicated himself in the 2019 memoir he co-authored, Compton Street Legend, the prosecutor said.
In Monday's testimony, a retired Las Vegas police officer said that he had asked Shakur who shot him as the rapper was being loaded into an ambulance and Shakur said something like "no, we'll take care of it".
Shakur died in a hospital six days later.
A former Las Vegas homicide detective said investigators pieced together the identities of Davis, Anderson and the other two men in the car through informants but could not find witnesses willing to officially identify them.
A former detective from the Los Angeles Police Department testified that Davis had briefly been a suspect in the 1997 shooting death of Shakur's east coast rival the Notorious B.I.G. but was later discounted as a possibility.
Sanft said outside court that he thought the 30 years that had elapsed would help Davis.
"The length of time is going to be a huge problem for people trying to recall things, to remember things," the lawyer said.
"That's just not how it works."
