Hernandez got treatment on his back Saturday and Sunday and threw on flat ground for a few minutes before Monday's game, hoping he'd be ready to go for Wednesday.
"He threw just OK today, not to the point where I felt comfortable bringing him back on Wednesday," manager Eric Wedge said. "He is feeling better, but no sense in pushing it."
Hernandez "tweaked" his back during the third inning of his last outing on Friday against the White Sox. He went just five innings in that game, tossing 85 pitches in a no-decision.
While the injury has lingered longer then the team would have hoped, Wedge said putting Hernandez on the disabled list wasn't considered.
Hector Noesi will start in place of Hernandez, after throwing only 68 pitches in his outing on Saturday against the White Sox.
"He feels like he can pitch at any point in time, but we are going to make sure we are careful with this, especially with the off-day on Thursday," Wedge said. "We'll see how he feels tomorrow and then go from there. We have multiple options because of the off-day."