The victims were identified as Alejandro Moreno, 39, of Desert Hot Springs, and Juan Meza, 28, of Cathedral City. No one else was hurt.
Witnesses Scott and Joan Barrick said they were checking out of the store when the brawl began between two women, each with a man. The women were near the checkout area, but the Barricks did not think the women had purchases.
One woman suddenly started punching the other woman, who fought back as blood flowed from her nose, said Scott Barrick, 41. The man who was with the woman being punched pulled a gun halfway out of his pocket, then shoved it back in, he said.
"He pulled his gun right next to me. I turned to look for my wife, and she was already hiding," Scott Barrick said.
"I was scared," said Joan Barrick, 40. "I didn't want to die today. I really didn't want to die today, and I think that's what we were all thinking."
The other man pulled a gun and pointed it at the first man but forgot to cock it, Scott Barrick said. The first man tried to run but was blocked by the line of people, then ran back toward the store's electronics section as the other man fired his gun, he said.
The first man reached a dead-end in electronics, turned around and ran toward an exit, pulling his gun and firing back, Scott Barrick said.
"He went up to the cash register, he went to put his hand on the thing and he just went phoomp," he said, indicating the man fell.
He said he did not see what happened to the other man.
Palm Desert Councilman Jim Ferguson said police told him two men with handguns shot and killed each other.
"I think the obvious question everyone has is who takes loaded weapons into a Toys "R" Us?" he said. "I doubt it was the casual holiday shopper."