The Cubs wanted to wait until Sunday morning to see how Prior felt before making a decision. Left-hander Glendon Rusch started in the series finale against the Milwaukee Brewers.
"We hope it's not too bad," Cubs manager Dusty Baker said. "These things can linger and stay around for a while."
Prior said he's hoping the injury doesn't affect him in the second half.
"We're going to play it by ear," he said. "This morning, I felt good getting up and sneezed and realized it wasn't getting any better. Hopefully, after four days, it'll be all right. I'm mad. ... I've never had a problem with my side."
O'Neal said strained obliques can be troublesome, and they want to be careful so Prior doesn't aggravate the injury and turn a seven-day injury into a four-to-six week thing. Prior will be reevaluated on Thursday when the Cubs have a workout at Wrigley Field.
What about his next start?
"I think it's questionable," O'Neal said. "These things are very tricky. You have to be able to sneeze, cough, normal things without any soreness. It's really not that sore, but there's enough soreness that whenever he rotates -- it's on the left side. He has to hit here. It's unfortunate we had to pull him out today, but it's better today than cost us four to six weeks."
If the Cubs decide to place Prior on the disabled list, they could backdate the start of that 15-day period to his last start, so he might only miss one start when the team comes back.
"I'm frustrated because I feel like I let everybody down," Prior said. "We won two games and had a chance to finish on a positive note. I'm more at a loss for words and frustrated and upset."
On Saturday, the Cubs got the news that Kerry Wood likely is out for the season because of a partial tear in his right rotator cuff. Now, Prior is sidelined.
"The goat's starting to look real," Prior said of the fabled curse of the billy goat. "My shoulder feels great, everything feels good, I'm feeling ready. I was starting to feel like I was right where I wanted to be. It keeps piling on."
"He's a big part of this team, especially when he's here and healthy," Baker said. "We've got to keep dealing like we've been dealing."