On Sunday night, Colin Kaepernick uttered the words his coach had used to console himself 17 years earlier, when a Hail Mary from Jim Harbaugh slipped out of Aaron Bailey's hands in the AFC championship game and kept the Indianapolis Colts out of the Super Bowl.

"We'll be back,'' Kaepernick said, his face still glum, unable to register any solace from the thought.

Kaepernick specializes in pith, and he had nothing more concise to say when a reporter asked what he'd take away from the 49ers' 34-31 loss, which left them just five yards shy of embracing the Lombardi Trophy. He had every reason to believe that he was right, too. The 49ers should be back in the Super Bowl soon and probably often. They could be the new Steelers or re-imagined Patriots of the next decade.

They came so close last year, within an overtime fumble of facing the Patriots in that Super Bowl. They came closer still to a championship this year, so close they could practically smell the inevitable pot smoke along San Francisco's parade route.

But Harbaugh had warned his team that "we'll be back'' amounts to gibberish. He knew as well as anyone. Bailey's dropped pass in 1996 was as close as Harbaugh would ever come to playing quarterback in the Super Bowl. Two years later, the Colts went 3-13, dumped Harbaugh and drafted Peyton Manning.

If that painful, desperate memory flitted through Harbaugh's head as he complained about the officiating after Sunday's loss, it must have turned off the circuit breakers in there. His insistence on reliving the final offensive play of his team's remarkable season, his pointless refusal to let go of that moment, could be the very thing that keeps the 49ers from following through on Kaepernick's vow.

As a coach, as the offspring and sibling of championship coaches, Harbaugh should have known better. He didn't just fail to show the desired "class and grass'' after the loss. He indulged a weakness, the kind that invades a team culture and slowly poisons it.

A year ago, when Kyle Williams fumbled the final punt return after muffing another in the NFC title game, his teammates stood by him. They took responsibility for all of the other shortcomings that had allowed the Giants to beat them.

Granted, it's much easier to stand up for a fellow player than to accept officiating flaws, especially when the teammate is as affable as Williams. But standing up is standing up, and making excuses is making excuses.    

When Harbaugh complained about the lack of a holding or pass-interference call on that final pass to Michael Crabtree, he flopped like a soccer player auditioning for a beverage commercial.

At half-strength, Harbaugh's sideline tantrums suffice to send the "I'm standing up for my guys'' message. At full strength, they call to mind an early-vintage Vernon Davis, overloaded with emotion and still in need of Mike Singletary's "cannot play with them, cannot win with them, cannot coach with them, can't do it'' speech.

Harbaugh has the freedom to commit more cosmetic errors than most coaches, without damaging his credibility among the players. He is the quarterback whisperer and the state-of-the-art defibrillator for teams in perpetual flat-line. He can get away with the tantrums via heat-of-the-moment understandings. Front-and-center complaints about officiating at a news conference, however, reflect a full-scale retreat from discipline.

After the loss, the 49ers' locker room yielded up quotes that sounded suspiciously like second-guessing the final offensive play calls of the game. Harbaugh shouldn't have been any more surprised by that than a profane parent who suddenly hears F-bombs spilling from his toddler's mouth.  

Kaepernick, at 25, had the presence of mind to emphasize his failures. He said he threw some passes too high, which was true, though minimally relevant. Few quarterbacks in the NFL, today or ever, could hope to pull a team back from a 28-6 Super Bowl deficit in the third quarter. This one had just nine NFL starts when he did it.

But his team lost, and Kaepernick looked inward in the manner that coaches crave, if not emulate. This is the same young man who after four fumbled snaps in a rainy Foxboro, interrupted reporters interrogating center Jonathan Goodwin to say: "Don't ask Goody about it. It was my fault.''

His maturity adds a lot of credibility to "We'll be back.''

Over the last 15 years, losing the Super Bowl has rarely led to an encore appearance within the next few years. In fact, only the 2011 Patriots have returned within five years of a Super Bowl loss. Seven of the 15 losers missed the playoffs the following year.

The 49ers, however, don't fit any mold. The roster is loaded with players who couldn't get past .500 under previous coaching regimes, and now form the core of an elite team. They reached the 2012 NFC title game with one quarterback and the 2013 Super Bowl with another.

The 49ers arrived at this year's postseason with a dramatically new personality. The offensive reconstruction with Kaepernick and the Pistol formation received due notice. The decline of the defense after tackle Justin Smith tore a triceps tendon in New England Dec. 16 largely escaped attention. The 49ers' defense kept its top-three ranking through the end of the regular season, but lost its intimidation factor.

By the time they reached the Super Bowl, they were respected but not feared. Smith was Ray Lewis' alter ego in 49ers colors, the big "Cowboy'' who devours opponents and disdains publicity. He couldn't play at his peak form, and a rookie Ravens guard, Kelechi Osemele, essentially neutralized him. The rest of the 49ers' defense, especially a secondary bereft of pass-rush help, had to pick up more than it could handle.

Unlike Lewis, the 33-year-old Smith has no plans to leave the game yet. He had also never been to a Super Bowl before.

Unlike Smith, Kaepernick cannot understand how hard it is to get there, to become a playoff perennial. From his view, it may not seem much more complicated than making instant oatmeal. Add a No. 7, stir, and plan to DVR the commercials and Beyoncé. You'll be busy when they're on live.

Harbaugh knew what he had in Kaepernick and had the guts to make him the quarterback when Alex Smith still topped the NFL in completion percentage. Outsiders were aghast, and he didn't care. His team doubted, just for a while, and he knew he'd be proven right. Kaepernick was special enough to merit the risk.

Second-guessing officials is pedestrian. It's fodder for fans and media. Harbaugh should consider it beneath him, beneath any coach. He indulged a whim. There are too many reasons that a team can come achingly close to a championship and then never have a shot at one again. Why take a chance on even one pointless indulgence, or one easily, almost reflexively, repressed whim?