Harden was replaced on the 25-man roster by right-handed pitcher Carlos Zambrano, who came off the DL on Friday following a left hamstring strain.
Harden was scheduled to pitch Saturday against the Padres. Right-hander Randy Wells will take Harden's spot and start Saturday night.
"I was feeling great and it was something that kind of hit me out of nowhere," said Harden, who is 4-2 with a 4.74 ERA this season. "Fortunately, it's not an oblique or nothing too serious that it's going to cost me a lot of time. Everything else feels excellent. My shoulder feels great and that's definitely positive.
"I didn't want to be in this situation, but hopefully it will be just a few games here," said Harden. "Wells has been doing a great job (0-0, 0.00 ERA in 11 innings). I'm sure he's going to take over and start for me. We'll just be ready to go next road trip."
Zambrano entered Friday with a 3-1 record and a 4.50 ERA this season, having allowed 19 earned runs in 38 innings across six starts. He has pitched six innings or more in five of his outings, including three during which he pitched seven innings.
Harden said he "definitely would be out there" if it were the last week of the season. "But at this point, with basically everything we've done in the offseason working with the shoulder and a lot of hard work, [the training staff] just wanted to take a few days and not turn it into five or six weeks on the DL," Harden said.
"It will be a couple of starts," said Cubs manager Lou Piniella. "He's got a mid-back strain. He felt it the last time he pitched a little bit and then when he threw on the side he stopped right away.
"We're putting him on the DL. Zambrano is taking his spot, so we get a starting pitcher and we lose one. Hopefully, it will be just a couple of starts and we'll get him pitching again.
"The amazing thing about it is that every time I've talked to him, he's feeling pretty good. But this thing crept up and now we'll have to deal with it. He'll miss a couple of starts and hopefully be back in the rotation."
Piniella said that Wells would take Harden's spot in the rotation on Saturday and that Ted Lilly would pitch on Sunday, Ryan Dempster on Monday, Sean Marshall on Tuesday and Zambrano again on Wednesday.
Sandy Burgin is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.