Left-hander Greg Smith, who posted a 1.50 ERA and had earned a bullpen spot, will replace Francis, who will be placed on the 15-day disabled list retroactive to Friday, manager Jim Tracy said.
Francis missed last season because of arthroscopic surgery on his throwing shoulder last February. This spring, he struggled with consistency -- but not with health issues -- before holding the Cubs to no runs and three hits in five innings on Thursday.
"What I'd been searching for all spring, I found it yesterday, and I was real excited to start the season," Francis said. "But like a lot of people say, this is another obstacle I'll have to jump over."
Francis, 29, said he was sore afterward, but thought it was because he pitched with an intensity he last displayed in 2007, when he was healthy and won 17 games in the regular season and two in the playoffs to help the Rockies to their first World Series trip.
Tracy had warned during the offseason that there would be some "up and down" with Francis' health. Francis thought maybe he would escape until Friday. Francis could not even have a catch on flat ground before the Rockies and Mariners spent 3 hours, 47 minutes playing to an 11-11 tie Friday night.
"Hopefully there's nothing significant. My heart and my gut are trying to tell me that is going to be the case, that we're just dealing with soreness," Tracy said.
Francis, who finished the spring 0-1 with a 5.64 ERA, said the pain is beneath the front of his shoulder, "under the armpit." The surgery was to the upper part of the shoulder. He doesn't know if he'll undergo an MRI. The plan is for him to stay with the team through the opening series in Milwaukee, then meet with doctors when the team returns to Denver.
"The way I had felt all spring, I had kind of put it out of my mind," Francis said. "I was going out and pitching, responding well every day. It snuck up on me, I guess.
"Maybe that's naive of me, thinking that."
Smith, 26, who joined the Rockies with pitcher Huston Street and center fielder Carlos Gonzalez in the deal that sent star outfielder Matt Holliday to the Athletics after the 2008 season, struck out 18 against six walks in 18 innings over five Cactus League appearances this year.
Last year, Smith, like Francis, didn't appear in the Majors. He underwent an elbow cleanup after the 2008 season. A bout with the flu during last Spring Training, and shoulder and back issues throughout the season limited him to 11 Minor League appearances.
Before Tracy made him the prime candidate for the final bullpen spot, it appeared he would be pitching at Triple-A Colorado Springs unless an injury occurred. Tracy said Friday night Smith "pitched his way onto the team."
"I never want to hear about bad health for anyone, especially a phenomenal guy like Jeff, who's worked so hard," Smith said. "But I'm excited to be able to throw in the opening series.
"Considering last year and that roller coaster, it gives me a sense of accomplishment to work my tail off throughout the offseason and this spring, take the opportunity that God has given me and be able to achieve a goal I set for myself."
Tracy expressed confidence in Smith.
"We're talking about a guy that a couple of years ago threw 190 innings in the American League," Tracy said. "He had a very respectable earned run average, was completely unhealthy a year ago, but has given us every reason to feel very strongly about the fact that his guy will do a very credible job for us."
Tracy said he hasn't determined if Smith's move to the rotation means the Rockies will place left-hander Joe Beimel on the Opening Day roster to complete the bullpen.
Beimel signed a Minor League with the club March 23 and has pitched well in two Cactus League games.
However, with right-handed setup men Rafael Betancourt and Matt Belisle having battled nagging injuries this spring -- Betancourt had shoulder stiffness and Belisle has dealt with periodic forearm tightness -- Tracy has struggled with the idea of adding another pitcher who might not be able to work consecutive days.
Other options are non-roster right-handers Justin Speier, Juan Rincon and Tim Redding, although the Rockies have already reassigned Redding to Triple-A Colorado Springs.
Thomas Harding is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.