In the top of the fourth, Arenado left a throw to first short, and he said the error resulted from his inflamed thumb.
"I've been dealing with it for about a month now … whenever [I] get jammed," Arenado said. "Even when you hit it on the barrel, but not squarely on the barrel, it just pushes against it. It's been hurting for awhile now. So today I actually hit the ball pretty good, too, and it just hurt, it strung real bad and when I threw that ball to first, I couldn't even finish."
DJ LeMahieu replaced Arenado at third in the top of the fifth and went 1-for-2 with a single.
Arenado is confident he'll be ready to start Friday against the Padres following Thursday's off-day. He tried wearing padding under his glove to reduce the pain, but didn't like the feel.
"I tried padding, but it just doesn't feel right," Arenado said. "So, I'd rather try to tough it out than change my whole thing."
Arenado was 1-for-2 before departing, shooting a single to right in the second and grounding out to third in his final at-bat.
Among the top candidates for the National League Rookie of the Year Award, Arenado has played Gold-Glove level defense and established a reputation for timely hitting. His eight game-winning RBIs are second most on the team and the 13 go-ahead runs he's plated are tied for fourth.
Arenado joins left fielder Carlos Gonzalez, pitcher Tyler Chatwood and center fielder Dexter Fowler as Rockies players who have battled some type of hand injury this year.
"You could see when he threw the ball across the infield, he had no feeling in his thumb," manager Walt Weiss said. "It's another guy that's day to day with a hand issue. It's pretty vogue around here. I think he'll bounce back in a couple days."
Arenado, 22, is batting .270 with 10 homers and 47 RBIs, and his .317 average in August was the highest of his young career.