Chatwood was removed for a pinch-runner. The team said he sustained a slight strain and cramping in his left hamstring, and will be re-evaluated Saturday. Chatwood pitched two innings and did not allow a hit.
Drew Stubbs had two hits for Colorado, including a triple.
The Mariners were held to four hits until the ninth, when their minor leaguers led the winning rally.
Seattle closer Fernando Rodney worked a scoreless eighth.
Both teams fielded everyday lineups.
Rockies: Colorado chose to let Chatwood bat even though the Mariners used a designated hitter. Chatwood tried to walk off the pain at third base with a trainer watching, but was pulled.
Mariners: Roenis Elias got his last start before his big league debut next week at Oakland. He allowed two runs on seven hits in five innings.
''I didn't have much control of the fastball,'' Elias said in Spanish.
''I thought it was going to be a disastrous outing for him,'' Mariners manager Lloyd McClendon said. ''That's usually the way it works when you tell a young man he's made the club, coupled with TV.''
MARINERS SET ROSTER
Elias, a 25-year-old rookie left-hander from Cuba who has never pitched above the Double-A level, won a spot in the starting rotation. Veteran left-handed reliever Joe Beimel also made the club, with the Mariners optioning pitchers Blake Beavan and Brandon Maurer to Triple-A Tacoma, along with reliever Lucas Luetge.
''I felt I was going to make the team because I worked really hard to get there. I fought hard to get this opportunity and I wasn't going to waste it,'' Elias said. ''I'm going to show that I can help the Seattle Mariners.''
Seattle opens Monday at Anaheim against the Los Angeles Angels. Felix Hernandez pitches the opener followed by Erasmo Ramirez on Tuesday, lefty James Paxton on Wednesday, Elias on Thursday at Oakland and Young on Friday against the Athletics.
The Mariners optioned infielder Nick Franklin to Tacoma, clearing the way for Brad Miller to open the regular season as the team's starting shortstop after a strong spring training in which he batted .439 in 19 games.
Abraham Almonte and rookie Stefen Romero are among the big league outfielders on the roster.
The Mariners re-assigned pitchers Zach Miner, Dominic Leone, Ramon Ramirez and Carson Smith to minor league camp. Catcher Humberto Quintero and outfielder Endy Chavez joined them, and outfielder Xavier Avery and infielder Carlos Triunfel were designated for assignment.
ROCKIES MAKE PITCHING MOVES
Right-hander Jhoulys Chacin is going to start the season on the 15-day disabled list with a shoulder strain, and Chatwood's injury, if more serious than reported, might create further problems in the starting rotation.
Chacin never pitched in a spring training game this year and was limited to bullpen sessions. He won't be joining the club in Miami for their season opener and instead will remain in Arizona to continue his rehab work.
Left-hander Boone Logan was also placed on the DL. Both moves are retroactive to March 21.
''I felt like Frankie at this point in time gives us our best shot as a starter,'' Rockies manager Walt Weiss said of Morales, who had a 2.21 ERA in six starts (20 1-3 innings) this spring. ''Jordan's going to be a big part of this club this year and well beyond.''
The Rockies were expected to announce their opening day roster Saturday.
PFP PAYS OFF
The Rockies' Lopez looks as though he has taken his pitchers' fielding practice seriously.
He caught a bounce well to his right off the mound and threw out the Mariners' Dustin Ackley in the third inning, and speared a line drive right back at him from Miller in the fourth to start a double play.
Rockies: Morales is the scheduled starter against the Mariners in Scottsdale, Ariz., on Saturday. On Sunday morning, the Rockies will fly to Miami and hold a workout after arrival.
Mariners: Young will make his Seattle exhibition debut against the Rockies on Saturday in Scottsdale. From there, the Mariners head to southern California to open the regular season.