One yard was the difference Sunday, enough to land the 2016 San Francisco 49ers on the wrong side of franchise history.
Quarterback Colin Kaepernick played a masterful game, slinging 296 yards and three touchdowns through the air while adding 113 more on the ground, but was taken down just short of the goal line on the 49ers’ last play to stomp out an unlikely comeback effort from San Francisco.
The moment was a bitter defeat for a 1-10 49ers team that has now lost the most consecutive games in franchise history, but who didn’t look the part against a streaking Dolphins team.
In what was billed as a running back duel, the Dolphins (7-4) and quarterback Ryan Tannehill took to the air to stomp out the 49ers. Tannehill completed 20-of-30 passes for 285 yards and three touchdowns.
Running back Jay Ajayi, who has been of the league’s hottest rushers as of late, was largely kept in check by the 49ers defense, gaining just 45 yards on 18 carries, while punching in his only score from two yards out.
Despite trailing 17 at one point in the fourth quarter, San Francisco made a late surge with a strong defensive effort and even better quarterbacking from Kaepernick.
The door was left open for San Francisco by poor clock management from the Dolphins, who refused to run the ball with a lead in the fourth quarter, taking just a few minutes off the clock with their final two drives.
San Francisco retained possession down a touchdown with just under two minutes to go, but couldn’t cap off the comeback, as Kaepernick’s final scramble of the game would be snuffed out by Miami one yard shy of punching in an equalizing score.
Carlos Hyde would earn his first touchdown since Week 5 for the 49ers, taking an 11-yard pass to the end zone. While receiver Torrey Smith and tight end Garrett Celek would round out the rest of the 49ers scoring.
In the battle between the pair of bruising young running backs, it was Hyde and the 49ers’ offense who struck first in Miami.
Amidst a chorus of boos from the Miami crowd, the controversial Kaepernick silenced his critics by leading the San Francisco offense on an eight-play, 62-yard touchdown drive that saw the 49ers firing on all cylinders offensively.
Kaepernick worked masterfully to open the passing lanes up with a steady mix of zone reads and play action passes. His 14-yard gain on the team’s first snap would help to keep the Miami defense on their heel throughout the duration of the series.
The quarterback would use this confusion to complete passes to his tight end, receivers and a mix of running backs before capping off the performance with an 11-yard yard play-action pass that worked Hyde open for an 11-yard touchdown.
With the Miami run game being bottled up by an uncharacteristically stout 49ers defense, Tannehill took to the air to work the Dolphins on to the scoreboard in the second quarter.
The streaking quarterback stretched the field on a swarming San Francisco defense with a deep, 46-yard connection to receiver DeVante Parker that would mark the team’s first big offensive strike thus far.
Miami would capitalize on the big play, pitching it out to Ajayi who would beat linebacker Eli Harold around the edge for a two yard score.
The touchdown would shift the momentum of the game, with the 49ers streaking offense beginning to grind to a halt while the defense that forced two early punts would begin to fold under the Dolphins’ aerial attack.
As has been the problem throughout the season, the 49ers would shoot themselves in the foot with a costly turnover that would lead to another Miami touchdown.
After working their way to the Dolphins’ 16-yard line, tight end Garrett Celek would lose the team’s league-leading 11th fumble of the season.
The turnover proved costly, as the rolling Tannehill would lead an increasingly dangerous Miami offense down the field on an 11-play, 86-yard drive that would conclude with yet another touchdown for the Dolphins, a 16-yard pass to tight end Dion Sims, for their first lead of the game at 14-7.
In what was supposed to be a run heavy approach for the Dolphins, the team rode into the half with a seven point lead on the backs of Tannehill’s 147-yard performance, good for a 118.5 passer rating.
The afternoon’s game looked to be in jeopardy of being blown wide open at the start of the third quarter, as the first play of the 49ers’ drive was tipped out of the hands of receiver Torrey Smith, and straight into the reach of linebacker Kiko Alonso.
Miami converted their second turnover of the day into more points, but the San Francisco defense would do well in holding the team to just a field goal after starting the drive on their own 26.
Despite the hold, the 49ers’ offense stood in desperate need of points against a Dolphins team finding their groove on both sides of the ball.
In what increasingly felt like a do-or-die scenario, Kaepernick would lead the team on a crucial second touchdown drive, with Hyde picking up a big gain on the ground early on to set up a redemption score for Celek on a play-action pass for four yard touchdown reception.
The score cut it to just a three point deficit for the road team. But as we’ve become accustomed to in the Jekyll and Hyde act of the 49ers, the ugliness of a 1-9 team reared its head late into the game.
As they had done earlier, the Dolphins continued to attack the 49ers’ defense through the air. And as they had done earlier, the team followed up an overturned gained by Parker with another touchdown, this time with receiver Kenny Stills spinning away from a poor route by safety Antoine Bethea for a 43-yard score and a 24-14 lead.
If that score built the 49ers’ coffin, then the next drive looked to add the nails.
Continuing to pound the 49ers defense through the air, Tannehill would sling three passes for 50 yards and his third touchdown of the day, capping the drive with a 15-yard score to Leonte Carroo for his first touchdown in the NFL.
The consecutive touchdowns would drop the 49ers to a 17-point deficit with time waning on the contest.
But as he had done throughout the day, Kaepernick would answer the call when the 49ers needed a crucial score.
With his team on the ropes, the veteran quarterback would sling his team back into contention, connecting on a 35 yard gain to tight end Vance McDonald that would help to set up an acrobatic one-yard touchdown from Smith in the end zone.
The drive marched San Francisco 75 yards in just under four minutes in an impressive rebuttal.
San Francisco would cut their lead to 31-24 with a field goal on their next drive after their defense made a clutch three-and-out stand that would zap just a minute-and-a-half off the clock for Miami.
Despite the three points, the 49ers looked lackadaisical in their approach, despite the winding clock and two-score deficit. While Kaepernick continued his strong, clutch play, the lack of tempo from an offensive coach known for his uptempo style was yet another head shaking moment from the 49ers.
After another crucial three-and-out from the 49ers’ defense, San Francisco would have one final chance with just under two-minutes to go in the game.
Kaepernick would put his best foot forward, converting a fourth-and-long effort to Smith and another clutch pass to Jeremy Kerley to land the team on the six yard line with six seconds to go.
A pass breakup to Smith would give the 49ers a final play. After being flushed from the pocket, Kaepernick would keep the ball for himself, but his efforts would be cut just short after being taken down near the goal line to end the game.
Shawn Whelchel is SFBay’s San Francisco 49ers beat writer. Follow @SFBay and @ShawnWhelchel on Twitter and at SFBay.ca for full coverage of 49ers football.