Chatwood issued a walk to Martin Prado to load the bases in the second on a pitch that sailed far beyond catcher Nick Hundley. Trainer Keith Dugger came to the mound with Weiss and pitching coach Steve Foster, and Chatwood quickly left to be replaced by righty Eddie Butler, who yielded a two-run Christian Yelich single for a 3-0 Marlins lead before finishing the inning.
Butler allowed six runs on nine hits and absorbed the loss.
Chatwood left the clubhouse and was not available for postgame interviews.
"He obviously wasn't of sorts, didn't look comfortable," Hundley said. "His movements weren't the same. They did a really good job of getting him out of there before he did more damage to his back. If you compensate with your arm, how valuable his arm is to us, you've got to be careful with that.
"He's such a competitor. To see him come out of the game, it wasn't good."
Chatwood was charged with three runs, giving up four hits and three walks with two strikeouts. Going into this season, Chatwood was a question mark since he underwent Tommy John surgery on his right elbow in 2014 and didn't pitch in 2015. He had the same elbow surgery at 16 years old, but it hasn't been an issue this year.
Even with Saturday's struggles, Chatwood has a 3.15 ERA, and he has emerged as a rotation leader.
"If you see how he works and how he goes about his business, to be in his clubhouse and not follow his lead, it would be not very smart and not a very wise career move," Hundley said.
Should Chatwood need to be replaced in the rotation is unclear. Butler is 2-3 with a 5.97 ERA in seven starts since being recalled from Triple-A Albuquerque. The Rockies could call upon righty Scott Oberg as a stopgap, since Butler will not be available for a few days. Righty Jordan Lyles is also in the mix.
Thomas Harding has covered the Rockies since 2000, and for MLB.com since 2002. Follow him on Twitter @harding_at_mlb, listen to podcasts and like his Facebook page. This story was not subject to the approval of Major League Baseball or its clubs.