"I am disappointed. I was looking forward to being in the Home Run Derby," said Cabrera, who feels discomfort in the back of his left shoulder.
Cabrera was initially in the starting lineup Sunday in the series finale at Dodger Stadium.
But minutes before the first pitch, the Marlins notified the umpires that Cabrera would not be playing in the afternoon contest. Because the lineup cards already were exchanged with the umpire, Cabrera technically was pinch-hit for, and he wasn't available.
While Cabrera is listed as day-to-day, he will not compete in the Home Run Derby for the second straight season.
The shoulder bothered him when he was taking swings in the batting cage.
"He came up to me and said, 'I can't get it loose,'" manager Fredi Gonzalez said. "It was a matter of 15-20 seconds later [after the lineup cards were exchanged]."
Cabrera, picked to his fourth straight All-Star Game, is batting .324 with 18 home runs and 61 RBIs. He belted an opposite-field home run off Derek Lowe on Saturday night.
But in the sixth inning of that game, Cabrera made a diving stop on a grounder by Andre Ethier. Cabrera threw out Ethier, but jammed his shoulder on the play. Still, he remained in the game, and got a single and scored a run in the seventh inning on Saturday. Then in the ninth inning, he lifted a sacrifice fly to deep right field.
Cabrera said he felt some soreness in the back of his shoulder after making the stop on Ethier's grounder.
"I felt it, but I didn't think it was going to feel this bad today," Cabrera said. "I tried to swing the bat. It hurt. It's sore."
According to Cabrera, he has been bothered by a sore shoulder on occasion dating back to last year.
Typically after a day or two, the discomfort goes away. Cabrera is hopeful he will be ready to go when the Marlins resume their second-half schedule beginning on Friday at home against the Nationals.
"From what I know from our training staff, he's had a little bit of history with this," Gonzalez said. "It takes a day or two, and then he's fine."
Cabrera competed in the Home Run Derby last season, connecting on 15 total while finishing third in the competition won by Ryan Howard of the Phillies.