Despite No. 1 seed, the 49ers confronted by questions heading into playoffs

The San Francisco 49ers earned the NFC West title and No. 1 seed with a 26-21 win over Seattle on Sunday, but they still had their weaknesses exposed

The San Francisco 49ers, thanks to a wild finish on Sunday night in Seattle that allowed them to clinch the No. 1 seed in the NFC, will have an extra week to rest up for the playoffs. But it shouldn’t be a week for the Niners to sit easily.

That’s because the 49ers, despite a harrowing 26-21 win over the Seahawks, head into the playoffs as a team with plenty of question marks. Gone are the Niners that began the season 8-0 and winning games by an average margin of more than 16 points with the NFL’s most potent defense. Instead, the 49ers that are turning the calendar over to 2020 are a group that have had their last five games be decided in the closing seconds.

Surprisingly, it’s been their defense that’s been the sore point for the 49ers in their 5-3 finish to the season. Through 12 games, coordinator George Saleh’s unit was giving up only 134 passing yards per game, the best mark in the league in 30 years. They led the NFL with 44 sacks in the first 11 games. But then Dee Ford, with 6.5 sacks, went down with a hamstring injury and has played just four snaps since Week 11. Over their last five games, the 49ers defensive line has reached the quarterback just four times. Nick Bosa, the run-away Defensive Rookie of the Year candidate for much of the season, closed out the year with one sack in those games.

The 49ers troubling defense rut began with a shootout in New Orleans, where they needed a key fourth-down conversion by tight end George Kittle to put them in position for a winning field goal in a 48-46 victory. Saints quarterback Drew Brees got to them to the tune of 349 yards and five touchdowns, three of them by early in the second quarter. Then, in Week 15, Matt Ryan led the Atlanta Falcons 70 yards in the last 1:42 and capped off the drive with a touchdown pass to Julio Jones in a Falcons upset in San Francisco. Last week, Rams quarterback Jared Goff threw for 323 yards against the Niners, who needed two 3rd-and-16 conversions on the game’s final drive to come from behind and win.

In the first half against Seattle on Sunday night, the 49ers looked back to their old selves, holding Russell Wilson and the Seahawks offense off the scoreboard. But the second half would play out much differently. Wilson went 18-28 in the second half for 178 yards as the Seahawks scored touchdowns on three straight possessions. And on their final drive, with the 49ers holding on to a five-point lead with the NFC West on the line, Wilson drove down inside the 49ers five-yard line before his completed pass to tight end Jacob Hollister was ruled down mere inches from the goal line.

That slim margin is the difference between the 49ers having to potentially play three games on the road to reach the Super Bowl, or holding home-field advantage throughout the NFC playoffs. But the elation of Sunday’s victory shouldn’t mask the fact that the 49ers are a team limping rather than sprinting into January.

The win over the Seahawks will feel good for one night, but head coach Kyle Shanahan and his team still have things to figure out. The good news is they have two weeks to do it.