He was originally set to start last Sunday against Tampa Bay but was scratched due to stiffness in his back. Hernandez left his outing Sept. 2 against Kansas City because of cramps in his lower back.
Now, manager Eric Wedge said Hernandez will not start against Houston.
"I guess you'd call it a minor oblique strain on the left side, if you had to put a label on it, but it was more just stiffness," manager Eric Wedge said.
Hernandez played down the injury Monday, saying he felt fine.
"Nothing serious. Just trying to be careful," Hernandez said.
Hernandez will throw from flat ground at the end of the week when the team travels to St. Louis.
"We'll just see how he feels and go from there," Wedge said. "We're not going to take any chances."
Hernandez is 12-9 with a 3.01 ERA this season. He's lost five of his last six decisions and has given up 38 hits and 24 earned runs during that stretch.
Although Wedge didn't say when Hernandez might pitch again, Hernandez said there was no question he would pitch again before the end of the season.
"Why would you want to shut me down?" Hernandez said. "I've got to go out there and do my best, try to finish strong. We're trying to win more games."
Right-hander Brandon Maurer will start Wednesday against the Astros in place of Hernandez.