Colin Kaepernick threw for 113 yards and a TD to Vernon Davis. Frank Gore ran 76 yards and a touchdown and Anthony Dixon added a short TD run that put Houston in a 21-0 halftime hole.
Randy Bullock kicked a 41-yard field in the third quarter for Houston's lone score. He also missed from 45 yards in the first quarter.
The game started similar to how the Texans' previous one ended.
Last week, Schaub threw an interception returned for a score that allowed Seattle to tie the game in the fourth quarter before Houston lost 23-20 in overtime. Fans in Houston have been calling for Schaub to be benched ever since, and some even burned his jersey and posted signs along city streets asking for backup T.J. Yates.
Schaub was 19 for 35 passing for 173 yards. Arian Foster also had 73 yards rushing on 17 carries for Houston.
The Texans failed to capitalize even when Schaub looked sharp. He regrouped to complete five of six passes for 32 yards on Houston's second drive that stalled deep in San Francisco territory after a pair of penalties on third down. Then, Bullock hooked his 45-yard attempt wide left.
Kaepernick took over and led San Francisco on a 12-play, 65-yard drive that spanned nearly six minutes. He completed a 9-yard pass to Anquan Boldin on third-and-9 before Gore's 1-yard TD run.
San Francisco left Schaub scrambling and stunned after Brock matched his career total for interceptions on two plays. Brock might've returned his second interception for a score had he not bobbled the ball in the air before getting tackled from behind by Johnson after 13 yards.
The 49ers wasted no time building an even bigger lead. Kaepernick scrambled 14 yards, Gore ran 18 yards on two carries and Dixon finished it off with 2-yard TD run put San Francisco up 21-0.
Eric Reid also dropped what should've been Schaub's third interception in the third quarter after Phil Dawson kicked a 38-yard field goal for San Francisco. And in perhaps the most mind-boggling interception, Jerod-Eddie dropped back to swipe Schaub's pass over the middle at San Francisco's 45.
Kaepernick then tossed a 64-yard TD pass to Davis.
Both teams entered with a 2-2 record and were trying to overcome obstacles. The defending NFC champion 49ers, though, looked like the only ones ready to revive their season.
Houston was trying to avoid its first three-game losing skid since the end of the 2011 regular season. And San Francisco was playing without several key defensive players for the second straight game.
All-Pro linebacker Patrick Willis sat out with a strained groin, cornerback Nnamdi Asomugha was sidelined with a knee injury and linebacker Aldon Smith was undergoing treatment for substance abuse.
AP NFL website: www.pro32.ap.org