Despite his strong play he'll head back to the bench as soon as Brian Hoyer can return.
''Hoyer is our starter,'' coach Bill O'Brien said. ''When he comes back, when he's healthy, he'll be in there and we've spoken to T.J. about that.''
The Texans (5-5) have won three games in a row for the first time since 2012. And they did it with Yates, who threw for 229 yards in his first start since Jan. 15, 2012, in the playoffs for Houston as a rookie.
Yates, who was signed on Oct. 28 after Ryan Mallett was released, started in place of Brian Hoyer who was out with a concussion.
Sunday's performance came after he took over in the third quarter on Monday night when Hoyer was injured and threw the game-winning touchdown in a 10-6 win over Cincinnati.
Yates understands his role with the team.
''If he's healthy, he's the guy, and I knew that situation going in,'' he said. ''He's got my full support. He's got everybody's full support.''
The game was tied in the third quarter when the TD pass by Shorts made it 17-10. Yates and Hopkins linked up for a 20-yard score on the next possession.
Hopkins beat Jets cornerback Darrelle Revis repeatedly before the cornerback left the game in the third quarter with a concussion.
He put the Texans on top when he got in front of Revis and grabbed a 61-yard touchdown reception to make it 10-3 with about three minutes left in the first half. The play came two plays after another big catch by Hopkins, where he again beat Revis and snagged the ball one-handed for an 18-yard gain.
''With my mentality, I'm 1-on-1 I'm going to win,'' Hopkins said. ''So no matter who's out there, I don't really care.''
Some things to know about the Jets-Texans game:
SHORTS DOES IT ALL: Shorts did a little bit of everything for the Texans on Sunday while running their newly unveiled Wildcat formation. He finished with 51 yards receiving, 26 yards rushing and 21 yards passing. Short, who was a quarterback early in his college career at Mount Union, took a lateral from Yates and tossed a 21-yard touchdown pass to a wide-open Blue to make it 17-10 with about eight minutes left in the third quarter.
The Texans stole a page out of Jacksonville's playbook on that one. It was the exact same play Shorts executed against Houston last year for the Jaguars.
Shorts was the star of that entire drive, grabbing a 16-yard reception on third-and-13 before grabbing a 35-yard reception on the next play. He took a direct snap and ran for 5 yards two plays before the TD throw.
STANDING BY FITZPATRICK: Ryan Fitzpatrick, who played after having surgery on his non-throwing thumb on Nov. 13, got New York within 24-17 with a touchdown run with 4 1/2 minutes left, but was intercepted on the next two drives to seal the win for Houston. Fitzpatrick was 19 of 39 for 216 yards with a touchdown against the team he started 12 games for last year.
Coach Todd Bowles wasn't happy with Fitzpatrick's performance on Sunday, but said his job wasn't in jeopardy.
''I'm still committed to Ryan,'' Bowles said. ''I just don't think he played very well.''
WATT ISN'T PERFECT ANYMORE: J.J. Watt had eight tackles and two sacks, but it was a day where his perfect record on offense was blemished. For the first time in his career, a pass was thrown to him that he did not catch when Calvin Pryor broke up the throw in the first quarter. It was the fourth time in his career he'd had a pass thrown to him and had reeled in each of the previous three for touchdowns. All of those scores came last season.
''I think anybody would be disappointed when you don't make a play ... that was a heck of a play by that guy,'' Watt said of Pryor. ''He earned it.''
BANGED UP JETS: Along with the injury to Revis, the Jets are also dealing with an injury to center Nick Mangold.
''Revis had a concussion and he's got to go through protocol, and Mangold's got lacerations in his hand between his pinky and his other finger that prevented him from snapping,'' Bowles said.
AP NFL website: www.pro32.ap.org and http://twitter.com/AP-NFL