Arenado, who has been bothered by a sore shoulder for a week, said he tweaked it while turning a double play in the third inning. He was covering second base on a play that was scored 3-5-3.
"After it, I had trouble throwing," said Arenado, who said he hopes to be back in the lineup Saturday. "It hurt too much to let it fly after that."
Arenado was 0-for-2 against Dodgers starter Kenta Maeda. He is hitting .307 this season with 29 homers and 82 RBIs.
Ryan McMahon replaced Arenado at third base and hit his first homer since June 20.
"It was Mac's night to give us a big swing," Rockies manager Bud Black said.
The Associated Press contributed to this report.