The 49-year-old was shot by a 57-year-old man, who then turned the gun on himself in the dining area of the restaurant on Gold Coast city's Siganto Drive, ABC reported.
Queensland Police Services' Detective Mark White said the man was taken to Gold Coast University Hospital with critical head injuries.
The man and woman were known to each other, he said.
There were no reports of any other injuries.
White said police were still in the process of verifying the identities of the man and the woman.
A man who witnessed the fatal shooting has described the moment the man walked up to the woman in the restaurant and put his arm around her before shooting her.
"I was about to go into the restaurant when I saw the couple struggling in their car."
"Then she got out ... she came inside. He sat in the car for maybe a minute then he got out and his expression didn't change for a moment," the man said.
"He just walked inside. He sort of showed the gun he had in his hand and I said to the guy that was next to me 'he's got a gun, we better step back' and he just walked inside, put his arm around her and just put the gun to her chest and shot her."
"And then he just did the same, he just put the gun to his own head and collapsed over the top of her," he added.
A statement from a McDonald's said the company was assisting police.