Now Jim Harbaugh's club hopes to return to the Super Bowl and come out on top this time around.
But are the Niners the best team in their own division, much less the very loaded NFC?
We'll soon find out. And to help us get started, we'll take a look at those division champions and the rest of last season's teams in the NFC that didn't finish with a losing record.
San Francisco 49ers (11-4-1): Third-year quarterback Colin Kaepernick will start the season and hopes to pick up where he left off during most of 2012. He'll have a new target in wide receiver Anquan Boldin, who makes his return to the NFC West. The running game is solid with Frank Gore and the defense, now with rookie safety Eric Reid, hopes to regain last year's early form.
Atlanta Falcons (13-3): Owning the best record in the NFC two of the last three seasons hasn't meant much to the Falcons, who haven't been to the Super Bowl since 1998. Pro Bowl quarterback Matt Ryan improves every year in terms of production and a new-look ground game now features veteran Steven Jackson. But can the defense learn to stop the run?
Green Bay Packers (11-5): Aaron Rodgers has put up enormous numbers the last two seasons but the Packers have been unable to get past the divisional round of the playoffs. More will be expected from the defensively-heavy 2012 draft class as well as rookie running backs Eddie Lacy and Johnathan Franklin. And winning the stacked NFC North is far from an afterthought.
Seattle Seahawks (11-5): Pete Carroll's team was seconds away from a date in the NFC title game last season but it wasn't meant to be. Second-year quarterback Russell Wilson now has versatile Percy Harvin to get the football to and workhorse runner Marshawn Lynch seems to be getting better with age. And good luck against arguably the best secondary in the NFL.
Washington Redskins (10-6): Quarterback Robert Griffin III was last season's NFL Offensive Rookie of the Year and head coach Mike Shanahan hopes he is ready on opening day following last season's knee injury in the playoffs. Albert Morris also enjoyed a banner debut season in 2012. The healthy return of defensive end Adam Carriker and linebacker Brian Orakpo helps.
Minnesota Vikings (10-6): From a combined nine wins in 2010-11 to 10 victories and a playoff appearance a season ago, Leslie Frazier's Vikings continue to build through the draft. In April, they added defensive tackle Sharrif Floyd, cornerback Xavier Rhodes and wide receiver Cordarrelle Patterson all in the first round. And there's that Adrian Peterson guy as well.
Chicago Bears (10-6): Changes in the Windy City as Marc Trestman takes over at head coach. Fixing the offensive line once and for all was a major priority during free agency and it continued with the drafting of Kyle Long in the first round in April. The defense did its job for the most part in 2012 but the Brian Urlacher Era is over (we think) in Chicago. Stay tuned.
New York Giants (9-7): A 9-7 record sure does not buy what it did a year earlier as the Giants went from NFC East and Super Bowl champions to second place and out of the playoffs. The defense disappointed in a big way in 2012 and the team was uncharacteristically busy during free agency trying to fix it. Second-year running back David Wilson is expected to step up.
Dallas Cowboys (8-8): A year after turning 7-4 into an 8-8 season, the Cowboys lost their final two games of the season and finished at .500 once again. Quarterback Tony Romo has felt the heat in more ways than one, hence the decision to draft center Travis Frederick in the first round. Can newest defensive coordinator Monte Kiffin fix a unit that continues to disappoint?
Everyone is a contender when the season starts. But are the 49ers the favorites just because they're defending conference champions? Is it one of the other teams mentioned above or perhaps some other club not listed that is truly the team to beat? Your best guess is?
Russell S. Baxter has spent the last 40-plus years watching football. He is the founder of ProFootballGuru.com, writes for numerous websites and publications across the country and is blessed with an encyclopedic memory. Ready to talk NFL? Follow him on Twitter at @BaxFootballGuru.
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