Yates, who was signed after Watson was injured, threw for 175 yards and two touchdowns in his first game since November 16, 2015.
Lamar Miller will also hope he can end the recent resurgence of the 49ers' run defense, which has given up just 152 yards in the last two weeks.
Savage took a hit from Elvis Dumervil that left him stiff and shaking on the ground.
Houston quarterback Tom Savage was cleared to re-enter Sunday's game against the San Francisco 49ers for one series after sustaining a concussion, raising questions about the NFL's procedure for evaluating such injuries during games.
After mustering four first downs over their opening four possessions, the 49ers caught fire in the second quarter after Garoppolo completed a 32-yard pass to Goodwin that set the stage for the first Gould field goal, a 52-yarder that pulled San Francisco even at 3-3 at the 6:31 mark.More news: Derrick Rose has bone spur, might need surgery
Texans coach Bill O'Brien is likely to face tough questioning on why Savage was allowed to return so quickly, particularly in a sport where concussion issues have been so much under the spotlight in recent times.
Savage had been benched earlier in the season in favor of Watson and has been 1-5 in his starts during the 2017 season. Savage attempted two more passes, both incomplete, in a three-and-out.
Tom Savage suffered an injury against the 49ers that forced T.J. Wrong! Savage returned to this meaningless game for a brief period before eventually leaving for the locker room. It appeared the wind was knocked out of him.
-Right tackle Trent Brown was declared inactive for the game after going through limited practice last week with a shoulder condition. When the Texans got the ball back after the 49ers ran six plays, Savage was under center.