The 49ers, including Joe Staley (74) , watch on the sideline as time runs out in regulation as Kansas City Chiefs lead 31-20 in Super Bowl LIV. (Chris Victorio | Special to the S.F. Examiner)

The 49ers storybook ending was lost in the last six minutes of the Super Bowl

In two Super Bowl starts, the 49ers offensive tackle now has two losses. But to him this one feels different.

MIAMI — Joe Staley was at a loss for words.

His eyes were red and his voice was soft. This wasn’t the fun-loving, jolly ole’ veteran that’s brought perspective and context to the 49ers’ unexpected postseason run this year.

In two Super Bowl starts, the 49ers offensive tackle now has two losses. But to him this one feels different.

“I’m just really sad,” he said, struggling to get the words out of his mouth. “You work your whole life to be a Super Bowl Champion and you get towards the end of your career and you realize how rare these opportunities are.”

For Staley — and the rest of the 49ers — Sunday’s 31-20 loss to the Kansas City Chiefs in Super Bowl LIV doesn’t feel like any of the defeats San Francisco has been handed over the last several years. They know this one was realistically in reach as they let immortality slip out of their grasp in just six short minutes.

“I think everyone felt very similar,” 49ers quarterback Jimmy Garoppolo said after the game. “It sucks losing like that — especially for a guy like Joe with just everything he’s been through … You can see it guys eyes in [the locker room]. It means something to them.”

Sunday wasn’t supposed to end like this for the 49ers. Throughout the entirety of the 2019 regular season, San Francisco made a habit of finishing games with clutch drives — with season-defining moments.

From George Kittle’s catch-and-run on 4th-and-2 against the New Orleans Saints to a touchdown pass to Jeff Wilson Jr. to come back against the Arizona Cardinals. The 49ers have had a penchant for producing when it mattered the most.

(The Super Bowl in photos)

It felt like that was the storybook ending that was coming for head coach Kyle Shanahan and company when San Francisco carried a 10-point lead into the fourth quarter at Hard Rock Stadium — even though Shanahan knew a two-possession advantage wasn’t enough.

“No you never feel good,” Shanahan said when asked how he felt heading into the final quarter of the game. “[Kansas City] can score very fast … That’s how that team is. They don’t do it every single drive. It’s just a matter of time.”

(The Chiefs and the 49ers were tied at the half)

San Francisco’s defense, which entered the evening as the league’s best postseason defense, allowing just 252.5 yards per game including 41.5 yards on the ground, had held the Chiefs to a mere 10 points through three quarters.

In addition, they had picked off Kansas City quarterback Patrick Mahomes twice, resulting in seven points off the turnovers. But when it came time to put their foot on the Chiefs throats, the 49ers failed to assert their dominance.

The possession after Mahomes’ second interception resulted in a punt — San Francisco’s first of the night — after their drive stalled near mid-field.

The Chiefs responded by matching 83 yards in seven plays, 44 of which coming on a 3rd-and-15 pass when Mahomes connected with a wide-open Tyreek Hill as the 49ers misplayed the deep ball.

“We just needed to be on top of it in that situation,” 49ers linebacker Fred Warner said. “[Mahomes] ended up timing it to air it out and we had no guys there to defend the play.”

Despite their lead dwindling down to just three points after Mahomes found tight end Travis Kelce for a one-yard score later on that drive, the 49ers had a chance to regain control of a game they had seemingly dominated for nearly 54 minutes.

Rather than sticking to what got it to the Super Bowl in the first place — a smothering running game schemed to gouge defenses with methodical chunk plays— San Francisco opted to pass on two consecutive downs. Both passes from Garoppolo fell incomplete, resulting in another punt.

San Francisco 49ers defensive back Tarvarius Moore (33) is called for pass interference on Kansas City Chiefs tight end Travis Kelce (87) in the 4th quarter at Super Bowl LIV at Hard Rock Stadium on February 2, 2020 in Miami, Florida. (Chris Victorio | Special to the S.F. Examiner)

To make matters worse, the 49ers had only taken one minute off of the clock, giving Mahomes and the Chiefs’ offense nearly six minutes to stage another comeback — their third in three playoff games to be exact.

Sure enough, Kansas City marched down field once again. This time, it was running back Damien Williams, who finished the game with 104 rushing yards and 29 receiving, that found the end zone on a five-yard pass from Mahomes.

“I think that was kind of the signature of the game,” 49ers fullback Kyle Juszczyk said. “They played better situational football. That’s what it boiled down to.”

The 49ers had one more chance to claim what they felt was their Super Bowl to win. With 2:44 to play, Garoppolo and the rest of the San Francisco offense had 85 yards to gain and one touchdown to score to recapture the lead.

On 3rd-and-10 at the Kansas City 49-yard line, the 49ers got their shot as wide receiver Emmanuel Sanders beat the Chiefs coverage down the middle of the field on a deep post route. But as Garoppolo let the pass fly, it sailed over Sanders’ head and onto the ground.

The very next play, Garoppolo was sacked, giving the ball back to the Chiefs, who scored another touchdown two plays later to firmly secure their victory.

“That’s exactly how it feels — disbelief,” 49ers tight end George Kittle said. “I thought we answered the call almost every single time this season … Just our mentality was we were going to finish this one out. Then when you don’t do it, you look in the mirror and ask why.”

San Francisco 49ers wide receiver Kendrick Bourne (84) stiff-arms Kansas City Chiefs defensive back Charvarius Ward (35) to try to get a few extra yards on a reception in the 4th quarter in Super Bowl LIV at Hard Rock Stadium on February 2, 2020 in Miami, Florida. (Chris Victorio | Special to the S.F. Examiner)

As Kansas City rushed the field in celebration of its first Super Bowl win in over 50 years, players on the 49ers sidelines had to be consoled. From rookie defensive end Nick Bosa, who cried into his hands to Staley, who walked away with tears swelling in his eyes, it was clear that this one hurt.

“It’s very hard to be in this moment right now,” Staley said. “The emotions are all still raw and real for me right now. I’m trying to answer questions, and I’m sorry if I’m not. Put yourself in my shoes for a second — it’s tough.”

As a 13-year veteran, Staley has been a part of many 49ers losses. On Sunday, though, hen says this one feels the worst — even when he compares it to his other Super Bowl loss in 2013.

It’s not clear whether Staley will be back next season or if the 49ers roster will look the same in other areas of their roster as several key players will enter the free agent market this offseason. One thing that is very apparent, though, is that the 49ers feel like they let this one slip away.

“Everyone is disappointed — and they should be,” Shanahan said. “I’m extremely proud of us and everything but this is going to take a little time to get over.”

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