MIAMI GARDENS, Fla. — Kyle Shanahan, graduate of the Andy Reid School of Clock Mismanagement and two-time Super Boal goat.

The 49ers coach butchered the strategy in the final two minutes of the first half of Super Bowl 2020, leaving two timeouts in his pocket and costing his team a chance to go into the locker room with a lead over the Chiefs. There also was no opportunity to make up the damage when the officials inevitably made a controversial call.

Predictably, coaching scared came back to cost Shanahan and the 49ers, when the Chiefs rallied for three fourth-quarter touchdowns and stole a 31-20 victory. After spending all week defending his aggressive management of the play-calling and fourth-quarter clock when the Falcons blew a 28-3 second-half lead in Super Bowl LI, Shanahan went too far in the other direction, even kicking a field on a fourth-and-2 when the score was tied in the third.

Here’s what happened: The Chiefs completed a 1-yard pass on third-and-14 just shy of midfield with 1:53 to go.

The 49ers could have immediately called their first timeout anticipating punt but instead let the Chiefs waste 35 seconds before the next snap, and only had 59 seconds to move the ball after a touchback.

The surest sign the 49ers were content settling for a halftime tie — a regrettable decision against the explosive Chiefs — was when Jimmy Garoppolo handed off for a total of 5 yards on the first two plays of the ensuing possession.

Even Reid — whose Hall of Fame coaching career is littered with clock mismanagement, most notably at the end of a Super Bowl XXXIX loss with the Eagles — must have been scratching his head on the other sideline.

So, Reid called a timeout with 20 seconds to go, hoping for a third-down stop, punt and Hail Mary magic from Patrick Mahomes. Had he figured out sooner Shanahan was coaching conservatively, Reid surely would have called after the first-down run, too.

The challenge seemed to wake up the 49ers and Garoppolo completed a 20-yard strike out to the 45-yard line, prompting Shanahan’s first timeout. The next play was a 42-yard pass to George Kittle down to the 13 with six seconds left.

Except … the officials flagged Kittle for a ticky-tack offensive pass interference penalty to negate the gain and lead to the 49ers kneeling to run out the clock. Which is what it seemed like they wanted to do the whole time.

“The receiver extends his arm and creates separation while the ball is in the air, therefore it is offensive pass interference,” senior vice president of NFL officiating Al Riveron said (to little satisfaction) on Twitter.

If the bizarre strategy — surely influenced with safety-net knowledge the 49ers would receive the opening kickoff of the second half — was just play keep-away from Mahomes and limit the number of Chiefs possessions, then why suddenly start pushing the tempo on third down?

If it was a sign of a lack of faith in Garoppolo — who threw a duck-and-chuck interception earlier in the half — then the 49ers have bigger concerns. Garoppolo is signed to a five-year, $137.5 million contract.

When Garoppolo threw only eight times in the NFC Championship Game, it was understandably excused as staying with a dominant rushing attack. He can deliver in the clutch when called upon, supporters said. His two throws when the shackles eventually came off further proved it.

It was just too little, too late. And Shanahan will continue to be haunted.

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