SAN FRANCISCO -- And on Sunday, for the first time in the Jim Harbaugh era, the 49ers were beaten up, knocked down and thoroughly humbled. Left with a feeling of helplessness, something they've never known in their 24 games under Harbaugh.

And they slipped into the evening curious about how they will recover after their comprehensive collapse in a 26-3 loss to the defending Super Bowl champion New York Giants at Candlestick Park.

"Plan-wise, obviously it wasn't the right one,'' Harbaugh conceded. "And you try to figure out what the next one will be.''

The Giants protected their quarterback, Eli Manning, while punishing San Francisco's quarterback, Alex Smith, who was dreadful one week after he seemed on a path to join the elite.

The Giants starved the 49ers running game while running effectively -- especially in the fourth quarter, when they absolutely needed to -- against a Niners defense that had been run-resistant.

Despite crafting a reputation under Harbaugh for playing smart and rugged and creative and with extreme ferocity, the 49ers were outplayed, outmuscled and out-coached.

"We're got a lot of work to do, on every phase of the game: offense, defense and special teams,'' cornerback Carlos Rogers said.

San Francisco's Super Bowl ambitions, which seemed so realistic, particularly after successive blowout wins over the Jets and the Bills, were bloodied by the reality of six New York sacks, three interceptions thrown by Smith and 342 yards accumulated by the Giants.

The Niners (4-2) still can come back and get where they want to go. But they had no idea they were so far away.

"We can learn a lot from this," linebacker Patrick Willis said. "One thing is that everything is not always going to go our way."

San Francisco had better learn quickly. The 49ers return to Candlestick on Thursday night to face NFC West rival Seattle, which moved to 4-2 with a win over New England that forced a three-way tie atop the division. Fourth-place St. Louis (3-3) is one game back.

Gone is any belief the 49ers would dominate the NFC West.

But San Francisco's biggest roadblock to Super Bowl clearly is New York. The 49ers came into the week knowing this was a statement game against the team that broke their hearts last January with a 20-17 overtime loss in the NFC Championship game.

Unlike that game, which was decided by breaks that went the way of the Giants, this one was decided by the precision and brute force of the Giants -- and an array of errors of the 49ers.

There were the three interceptions thrown by Smith, leading to 13 New York points. There were two missed field goals by kicker David Akers, costing the 49ers six points; a dropped interception by Carlos Rogers; a 66-yard kickoff return allowed by the coverage unit; and the 116 yards surrendered to running back Ahmad Bradshaw.

Along the way, the Giants punished Smith and backup Colin Kaepernick, made Vernon Davis disappear and Frank Gore irrelevant.

It was unlike any other game in the Harbaugh era, during which the five previous losses were by an average margin of 5.8 points. Always, there was a sense the 49ers were not out of it, were in it until the very end.

Not this time. Fans were restless early in the third quarter and started filing out shortly thereafter, when the Giants took a 23-3 lead. They hadn't seen such ineptitude since the worst days of Mike Singletary or Mike Nolan or Dennis Erickson.

"It just hurts so much because we are used to winning, especially since last year," Davis said. "And to lose it just hurts."

So comprehensive was this speed-bagging it's conceivable the Giants have set up residence inside the heads of the 49ers.

"The statement we made today," said Giants receiver Victor Cruz, who caught a 6-yard touchdown pass, "was that we are here to stay."

For the 49ers, this was a blast from the ugly past, a reminder of indignities endured during their eight seasons away from the playoffs.

"The plan wasn't the best plan," Harbaugh said. "And we'll work to make a good one this week. (It) wasn't a great day for any of us.

"I don't know that I have the lesson learned right at this moment. But we'll think through it and see if we can get it corrected."

The 49ers thought they were beyond the days of being too sloppy and not strong enough. The numbers supported them. It has been safe throughout this season to presume they are among the top five teams in the NFL. Maybe they still are.

But not when they line up against the Giants, who swaggered out of town after burying most everything we thought we knew about 49ers.

Contact Monte Poole at mpoole@bayareanewsgroup.com. Follow him on Twitter at twitter.com/1montepoole.