The Texans had placed Watt on injured reserve Wednesday, meaning he'd be out a minimum of eight weeks.
Coach Bill O'Brien said Watt had re-injured his back and putting him on IR was the best thing for his long-term health. At the time, it was unclear if he would need surgery.
The reigning Defensive Player of the Year missed training camp and Houston's four preseason games after surgery in July to repair a herniated disk in his back. He started each of the team's three regular-season games and got hurt again last Thursday against the New England Patriots.
In a message to fans on Twitter on Wednesday, after he was placed on IR, Watt tweeted that he "will be back."
"I haven't missed a game since my sophomore year of high school," Watt said. "This won't be fun, but it is necessary in order for me to return to 100 percent and play at the level that I am capable of playing at.
Watt, who led the NFL with 17 1/2 sacks last season, has 1 1/2 sacks this season to give him 76 for his career.
Information from ESPN.com's Sarah Barshop and The Associated Press was used in this report.