It had been reported earlier that Johnson had planned to play.
While Johnson was held out with an injury, Texans running back Arian Foster failed to start due to a "coach's decision."
"I didn't handle my business off the field, I got disciplined for it, and rightfully so," Foster said. "I take full responsibility and I apologized to my teammates for it, and it won't happen again. And we're all about moving on here. I slipped up, and I'm assuring it won't happen again."
Neither Foster nor coach Gary Kubiak would say what went into the decision to bench the NFL's leading rusher for the first 23 minutes against the Raiders.
"Bottom line, we all have responsibilities and over the course of the past few weeks he's neglected responsibilities, he's been unaccountable in a couple of situations," Kubiak said. "When that happens you've got to learn a lesson, pay a price. I'm disappointed in him, but proud of him coming back and playing well today."
Foster got on the field in the second quarter then made up for lost time, scoring on a 74-yard run and a 10-yard catch in the second half of Houston's 31-24 win over Oakland.
Backups Steve Slaton and Derrick Ward filled in nicely for Foster in the early going. Ward scored on a 33-yard touchdown run on Houston's opening drive and Slaton had 47 yards from scrimmage in the first quarter.
Johnson leads the Texans with 19 catches for 255 yards and one touchdown. Jacoby Jones started in his place against the Raiders.
"The biggest thing is making sure that ankle feels well. I'm not going to do anything to set myself back," Johnson told the Houston Chronicle. "We still have a long season ahead. I don't want to re-injure it again. It got twisted up pretty good in the Dallas game."
Information from The Associated Press was used in this report.