Niners top 'Hawks, but is Smith's confidence finally beyond saving?

You can't help but wonder about Alex Smith's psyche after the coaching staff left him on the field but took the ball out of his hands down the stretch in a 13-6 victory over the Seahawks in Candlestick Park.

Smith threw three interceptions last Sunday in a home loss to the Giants, then was picked off again five plays into the fourth quarter against Seattle -- in a physical showdown that would determine first place in the NFC West. The 49ers were leading by four at the time and faced a third-and-goal from the 7. Smith took the snap in the shotgun, rolled to his left, then fired a pass across his body toward wideout Randy Moss in the corner of the end zone.

One problem: Cornerback Brandon Browner was lying in wait and stepped in for the interception.

The 49ers got the ball back after forcing a three-and-out and drove to the Seattle 13, and that's where the possible deconstruction of Alex Smith began. On second-and-7, offensive coordinator Greg Roman called a run to Kendall Hunter. He gained 8 yards, but a tripping penalty on right tackle Anthony Davis negated the play and set up a second-and-17. Instead of going with a pass play, the 49ers ran Hunter up the middle for 10 yards.

On third-and-7, a passing situation in almost every playbook, Smith took the snap in the shotgun and slid slightly to his left before taking off on a planned scramble. It gained 3 yards and set up a field goal.

So on their first offensive series following Smith's interception, the 49ers ran seven plays, six of them rushes, including on second-and-17 and third-and-17. His one pass was for 3 yards to Hunter, which basically was a handoff.

At the risk of stating the obvious, the 49ers coaching staff didn't trust Smith to make a play in that situation. It will say otherwise in the days and weeks to come, just as coach Jim Harbaugh did Thursday night.

"Alex had a very good game, made really good decisions," he said. "He was fantastic for us all night ... did a great job of getting us into the right play. Played with a lot of poise. Made some conversions for us and thought he played extremely well."

Smith was not fantastic, nor did he play extremely well. He played tentatively, like someone who was concerned with making a mistake. In finishing 14-of-23 for 140 yards and a touchdown and interception, he looked like someone who feared he was one mistake from possibly watching from the sideline, even if that wasn't the case. Consider:

Facing a third-and-9 from his 18-yard line late in the first quarter, he had Michael Crabtree open on a post route and Kyle Williams clear in the flat. He opted to scramble and was sacked. Perhaps he knew he was in field-goal range and didn't want to lose valuable yards that could cost the 49ers a chance at the 38-yard field goal that tied the score at 3. Or maybe he didn't spot his open receivers. Whatever it was, things only got worse from there.

At that point the playbook looked as if it didn't have pass plays for which the ball traveled more than 5 yards. His next seven pass plays after the scramble/sack ended as follows: incompletion, 6 yards to running back Frank Gore, 6 yards to Gore, 1 yard to Crabtree, incompletion, incompletion, sack.

Fantastic? Extremely well? Seven of his 14 completions to running backs? You be the judge.

Harbaugh has to accept some culpability if Smith's confidence is shaken. His decision to allow Roman to rotate second-year backup Colin Kaepernick into the lineup for a specific play or series of plays throughout the season could easily be interpreted as a lack of confidence in Smith, who has been under fire for most of his career. Smith is too classy to say if he's bothered by sharing playing time, but only one other team uses its backup as often as the 49ers have used Kaepernick, and we know what a circus the Jets are.

It has been said that if you have two quarterbacks, you don't have one. San Francisco is threatening to prove that point. Smith proved critics wrong last season in leading the 49ers to the NFC Championship Game, but almost immediately the organization began sending him what he could interpret as mixed messages.

First, the sides couldn't come to terms on a new contract before free agency started. Then the team pursued free-agent Peyton Manning, who spurned them to sign with the Broncos. If Smith is really your guy, do you fly cross-country to watch Manning work out with an interest in signing him? And if he's really your guy -- and you know how much it means for him to know that the organization is completely in his corner -- do you continually pull him from games to give snaps to Kaepernick? Is it merely a coincidence that Smith's interception against the Seahawks came one play after Kaepernick replaced him for a snap?

This much we know: Since scoring 45 points against Buffalo, the Niners have scored just one touchdown in two games, and it's a roller-coaster ride that Smith is accustomed to in more ways than one.

"I feel like that's the NFL -- that's what it is, it's the ups and downs," he said. "You have to be able to ride them out. Really within the building, with the locker room, you've got to. You can't have those ups and downs. I know you guys like to write about them and make a big deal about it, (but) you have to move on to the next opponent and get ready. Couple of weeks ago you break records and last week it wasn't good at all offensively. Today, you know, we ran the ball really well. It wasn't a pass game, but we got it done."

True, they got it done for a night. But to achieve their goal of reaching and winning a Super Bowl, they're going to need more from Smith. Whether they get it could ultimately decide their season.