Colin Kaepernick looked more uncomfortable than he ever has as San Francisco's starting quarterback, but the bigger issue was the team's defense.
Seattle scored five offensive touchdowns in seven possessions and converted 11-of-12 on third down (not counting possessions ending in quarterback kneel downs).
Going back to last week against the Patriots, the 49ers defense has allowed nine touchdowns and a field goal in 14 possessions.
The one silver lining is that eight of those touchdowns were scored with Justin Smith off the field. If he can return in time for the playoffs, maybe the San Francisco defense will find its mojo again.
So, either the 49ers defense is not up to the challenge against playoff-caliber offenses, or Smith makes the defense about 25 points per game better.
Believe what you will, but I'd argue this is the most uneasy 49ers fans have felt since Jim Harbaugh took over the reigns.
One thing's for sure: Seattle has one of the best home-field advantages in the NFL, and as long as San Francisco wins against the Arizona Cardinals on Sunday, it won't have to play in the Emerald City again this year.
Depending on the results of this weekend, the 49ers could end up with either the No. 2, No. 3 or No. 5 seed in the NFC playoffs.
Let's take a look at San Francisco's potential playoff seed and the outlook of the team going into the postseason.
Route to the No. 2 seed
The 49ers (10-4-1) need a win and a Green Bay Packers loss to secure the No. 2 seed and a first-round bye in the NFC playoffs.
Green Bay (11-4) has won four in a row, with a win against Minnesota at Lambeau Field included in that streak.
But traveling to Minneapolis and picking up a win is an entirely different matter. Just ask the 49ers.
Behind three touchdowns by Christian Ponder (two pass and one rush), the Vikings beat San Francisco 24-13 in Week 3 of this season.
Overall, the Vikings (9-6) are 6-1 at home this year. They have won three in a row and need to beat Green Bay to make the playoffs.
Likelihood: 40 percent
No. 3 seed
This is the seed the 49ers will secure if they win the NFC West and the Packers finish with a better record.
San Francisco's three most likely opponents for this game are the Chicago Bears, New York Giants or Washington Redskins (in the unlikely scenario that the Seahawks lose, the 49ers lose AND the Vikings win, San Francisco would play Minnesota).
Of the three likely opponents, the 49ers have already destroyed the Bears (9-6) and been dismantled by the Giants (8-7).
When the Bears were whupped by the 49ers in Week 11, they were without Jay Cutler, their starting quarterback.
Still, it looked like Chicago simply didn't match up with San Francisco's dominant pass-rush. Of the three opponents, Chicago is the one the 49ers should want to see.
Likelihood: 55 percent
No. 5 seed
This is the seed the 49ers will end up with if they lose and the Seahawks win.
San Francisco would go on the road and play the winner of Sunday's showdown between the Dallas Cowboys (8-7) and Washington Redskins (9-6) in this scenario.
Arizona might be the worst team in the NFL right now. Expect a bounce-back performance from the 49ers this Sunday.
Likelihood: 5 percent
San Francisco will likely end up with a first-round bye or a first-round matchup against the Chicago Bears.
Either way, I believe a Divisional Round showdown against the Packers is in the cards.
As long as Justin Smith is healthy and productive, the 49ers should at least have a chance against Green Bay.
The other side of the NFC bracket could go a number of ways. Seattle and Atlanta are hot right now, and Robert Griffin III and Tony Romo are both playing at a high level.
So, which team will represent the NFC in the Super Bowl?
I'd say it's a toss up between the Falcons, Packers, 49ers and Seahawks (10-5).
To reach the pinnacle of the NFL, San Francisco must play with more consistency and break the trend of falling short every third game.
The 49ers are certainly not the overwhelming favorite anymore, but they still have the talent to make the Super Bowl.