Soto felt some discomfort when he threw to second in the third trying to get Houston's Kaz Matsui, who was safe. The problem was not related to Soto getting hit by a pitch on the left side by Houston's Wandy Rodriguez in the second inning.
Expect Koyie Hill to start Wednesday in the Cubs' series finale.
"I kind of over-exposed my shoulder a little bit," Soto said. "There was a little discomfort in my shoulder. I felt some weakness in it, and I felt I didn't have a shot if somebody else [tried to steal]. I need to keep up my exercises, and we'll see how it is in a couple days."
Soto said he had the same problem in Spring Training and doesn't expect to miss much time.
"You never know," he said when asked how long he'd be sidelined. "I just have to stay on top of my exercises, and I'll be all right in a couple days. As long as I stay in good shape and do my exercises, it won't happen again all year."
Soto predicted he could play Wednesday if it was a "super emergency." Shortstop Ryan Theriot was behind the plate catching Aaron Heilman when he was warming up in the ninth. When asked who the emergency third catcher is, Lou Piniella said: "Me."
The Cubs would probably use Theriot or Mike Fontenot over their 65-year-old manager.
"Right now, where we're at, I feel I won't help the club if I go out there and I'm not 100 percent," Soto said. "I want to make sure I get my shoulder straight and help the club."
This year, the Cubs opened the season with no players on the disabled list for the first time in 23 years. The last time they broke camp this healthy was 1986, and the first player to be sidelined with an injury that year was Lee Smith on April 21.
The Cubs feel they can pick up the slack.
"I think tomorrow we have a righty, so I think Koyie Hill will do a good job," Alfonso Soriano said. "He's a very good guy, and I think he knows how to call a game. I think for a couple days he can do the job."
"That's the nice part when you have such a deep lineup," Cubs pitcher Ryan Dempster said. "The other guys pick each other up. Hopefully, it's just a little bit of inflammation and he's back real soon. Koyie did a good job all spring and did a great job last year. He'll do real well this year whether it's playing one game or playing a few. Hopefully, we can get Soto back out there right away."
Carrie Muskat is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.