SANTA CLARA, Calif. — Alex Smith is the San Francisco 49ers’ starting quarterback again, apparently to stay.

“We’re not going to be a flavor-of-the-month kind of team,” Coach Mike Singletary said.
Singletary announced Smith’s promotion over incumbent Shaun Hill on Monday, a day after the former No. 1 pick nearly rallied the 49ers from a three-touchdown deficit in a 24-21 loss to the Houston Texans.
Smith completed 15 of 22 passes for 206 yards and three touchdowns in just one half, igniting an offense that had sputtered all season.
His first start in almost two years will come Sunday, when the 49ers (3-3) face Peyton Manning and the Indianapolis Colts (6-0).
Singletary broke the news to both quarterbacks Monday morning.
“I’m just as proud of myself now as I was three days ago,” Smith said. “I just continue to try to get better. That’s being a quarterback in the NFL. There are going to be ups and downs. You just have to be levelheaded and stay consistent.”
Singletary gave Smith the nod a day after another rough afternoon for Hill, who threw for just 45 yards in the first half as the Texans roared to a 21-0 lead. The 49ers liked Hill’s smart play to start the season, but defenses quickly deduced that his arm would not beat them deep.
Opponents started stacking the tackle box with eight or nine defenders, and the 49ers’ slumping offensive line was unable to hold off the onslaught.
That’s why Singletary made the move to Smith, whose superior physical gifts could make defenses back off.
“Hopefully, we are able to make them get the heck out of the box and play us fair,” the coach said. “We certainly have some playmakers out there, and having a quarterback that can consistently make the throws that Alex can make gives us a chance to really branch out a bit and open things up.”
Smith’s arm strength has always been an asset, but the rest of his game has been slow to develop. As Urban Meyer, his college coach at Utah, famously said, Smith is “nonfunctional” until he fully understands an offense. (”Definitely the truth,” Smith said with a laugh Monday).
During his first venture as a starter, Smith could be jittery in the pocket, slow with his reads and inaccurate with his throws. Entering this season, Smith had 19 touchdown passes to 31 interceptions. His career passer rating of 63.5 is far below the 79.6 rating that has earned Hill a benching this season.
Singletary said Monday that Smith just needed more time to put things together. That included five-plus games of watching from the sideline this season.
“I don’t think it’s the same old Alex,” Singletary said. “I think he has matured. I think he’s grown, and I think he’s ready to play. We’re going to find out.”
Smith looked rejuvenated against the Texans, making quick decisions and throwing the ball with velocity unseen since his two shoulder operations. His first regular-season pass in nearly two years was a 17-yard fastball to rookie Michael Crabtree.
The entire offense seemed to perk up under his command. Smith went on to become the first 49ers quarterback to throw at least three touchdown passes in one half since Jeff Garcia threw four in the first half against Arizona on Dec. 7, 2003.
Hill, meanwhile, acknowledged he was unhappy with the move. His demotion comes a year to the day after taking over the job. Singletary inserted Hill in favor of J.T. O’Sullivan on Oct. 26, 2009. That was the famous “I Want Winners!” game.
Hill guided the 49ers to a 3-1 start this season, but they were outscored 66-10 over his final six quarters. “I was disappointed,” he said of the news, “but I understand (Singletary’s) situation, too.”
Hill and Smith are close friends. Each said they will continue to root for the other.
“Neither of us has exactly had it easy in this league,” said Hill, the longtime backup. “It’s frustrating. It’s upsetting. It’s tough to take.
“But it’s not going to hold me down. Nothing ever has and nothing ever will.”