Hernandez -- who has been dealing with tendinitis in his left hand, a condition that has affected his ability to grip a bat -- was hitting .215, with four homers and 15 RBIs in 27 games this season.
"Rather than keep going back and forth like we have been doing, we'll just take the opportunity to give him time and see how [the healing process] goes," manager Jim Tracy said.
Wil Nieves replaced Hernandez on the active roster after the Rockies selected his contract from Triple-A Colorado Springs.
"Wil prides himself a lot on the defensive end, and he's very good at it," Tracy said. "He has a lot of energy and a good feel for game calling. I'm anxious to see how that plays out with some of our young starters."
Nieves, who will wear No. 41, began the season with Colorado Springs and has hit .299 with four doubles, three homers, 14 RBIs and 14 runs scored in 28 games at Triple-A. This will be the 34-year-old's fifth Major League team since 2002, as he previously played with the Padres, Yankees, Nationals and Brewers.
Nieves is a career .221 hitter with 32 doubles, two triples, five homers and 73 RBIs in 282 Major League games.
The Rockies also transferred infielder Hector Gomez (groin strain) from the 15-day disabled list to the 60-day DL; their 40-man roster remains full.