Koehler, who threw seven scoreless innings in a 2-0 win over the Giants on Tuesday, will remain on his normal schedule, getting four days of rest between starts.
For Fernandez, it was expected that he would skip one start after the All-Star break. The team did a similar move in the first half.
The objective is to scale back Fernandez's workload in hopes that he will pitch in the 180- to 190-innings range and also be available for the postseason, should the Marlins make it. Currently sitting at 137 2/3 innings in 22 starts, he is tracking toward about 185 innings in 30 starts in the regular season.
It has not been announced when Fernandez will rejoin the rotation.
But the revised rotation still has right-hander Andrew Cashner starting for Miami in the series opener with Chicago on Friday, and left-hander Adam Conley starting on Saturday.
Had Fernandez stayed in turn, Koehler would have opened the road series on Monday at Cincinnati.
The club hasn't announced who will make that start, but it could be David Phelps, who went on Wednesday in Miami's 1-0 loss to San Francisco.
Koehler has been the Marlins' most effective starter the past four weeks, posting a 3-0 record with a 0.67 ERA (two runs in 27 innings) in his four starts.
Joe Frisaro has covered the Marlins for MLB.com since 2002. He writes a blog, called The Fish Pond. Follow him on Twitter @JoeFrisaro and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.