Baker injured himself when trying to turn a double play on a ball hit by the Nationals' Laynce Nix in the first inning. Baker fielded it cleanly but slipped as he pivoted to throw the ball to shortstop Darwin Barney who was covering second base. The ball sailed into left field, allowing two runs to score. The Nationals won, 3-2.
Blake DeWitt replaced Baker at second.
"I slipped on that double play ball. My back foot went out and my back started to spasm," Baker said. "Then it locked up my whole back. It (stinks). It's one of those things. You want to grind through it but at the same time if you push it you're going to be out for a couple of weeks."
Cubs manager Mike Quade said Baker is day to day, a phrase he has come to know well this season.
"He may miss a couple of days," Quade said. "Day to day. It's become my middle name."
Earlier in the day, the Cubs placed pitcher Marcos Mateo on the disabled list and recalled 38-year-old pitcher Ramon Ortiz from Triple-A Iowa. Ortiz made his Cubs debut on Tuesday against the Nationals. Fellow pitchers Carlos Zambrano is on the DL, and Ryan Dempster missed Sunday's scheduled start with complications from a gastrointestinal disorder.
Baker was on the disabled list earlier this season with a strained left groin.
ESPNChicago.com's Bruce Levine contributed to this report.