The final 31 seconds went the Bears' way, allowing them to celebrate their first win of the season. But back at Halas Hall on Monday, Nagy and the team will look closely at the first 59:29 of the game. There was plenty to take away and correct.
Let's break down the most important takeaways.
The game plan that Nagy had for the Bears' season-opening loss was a reflection of his belief in quarterback Mitchell Trubisky. And so too was Nagy's plan for Trubisky on Sunday, as it revealed the diminished confidence the coach has in his quarterback.
Nagy set Trubisky up with constant dropbacks and run-pass options in the opener, a 10-3 loss to the Packers. It resulted in Trubisky throwing 45 passes while the Bears' top three running backs recorded 11 carries. Against the Broncos, Nagy noticeably altered the game plan.
Trubisky was 16-of-27 for 120 yards, not surpassing the 100-yard mark until he hit Allen Robinson on a 25-yard strikes that set up Eddy Pineiro's game-winning field goal with one second remaining. After implementing plenty of RPOs in the opener, the Bears ran few in their second game.
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The Bears rushed 29 times for 153 yards against the Broncos, including 18 carries for 62 yards by rookie running back David Montgomery. Those rushes came primarily on designed plays instead of RPOs. Even when the Bears weren't getting production from the running game in the first half, Nagy remained committed to it.
Nagy is well aware of the deficiencies in the Bears' passing attack, which averaged 4.4 yards per dropback after managing 4.6 yards against the Packers.
Moving forward, Nagy and the Bears may be best suited remaining committed to the run -- and leaving Trubisky to just manage the game.
In a game with so many decisive moments, it's easy to forget some. Bears cornerback Kyle Fuller's interception in the fourth quarter was one such example.
A year after posting a career-best seven interceptions, Fuller recorded his first of the season on a pass deflected by safety Ha Ha Clinton-Dix. It was similar to many of Fuller's picks from 2018 -- a byproduct of the constant film study from one of the most dedicated students in the Bears' locker room.
Fuller recognized the cross between Broncos receivers Emmanuel Sanders and DaeSean Hamilton and saw quarterback Joe Flacco was ready for a quick release. He shifted gear forward before Flacco let go of the football and corralled the deflected pass.
"Hey, Ha Ha, appreciate you," Fuller yelled to his teammate in the victorious locker room. "He got an assist."
At the time, Fuller's interception maintained a 13-6 lead for the Bears with under five minutes remaining. It cleared out many seats inside Empower Field -- even though the game was far from over.
After the Broncos converted their two-point conversion to take a 14-13 lead with 31 seconds remaining, 24-year-old kicker Eddy Pineiro realized an opportunity that he desired could soon await. He desperately wanted to prove he could handle the pressure of a big moment by winning a game for the Bears.
Nagy and the Bears could only wonder how he would respond to the tension. For months, the Bears had simulated pressure situations in practice -- field-goal attempts in front of a 90-man roster and "Augusta silence" on the back field of Halas Hall -- but this was different.
Pineiro began warming up his leg immediately after the Broncos tacked on those two points. When he ran out with one second remaining for the 53-yard attempt, he did so with confidence.
Pineiro had approached Bears special teams coordinator Chris Tabor with a message before the kick.
"I go, 'Coach, I got you. This one's for you,'" Pineiro said. "Just went out there and hit my kick."
It was an important step for tight end Trey Burton to take the field with the Bears, but it's clear he still isn't quite right.
Just two weeks removed from a groin strain, Burton played in 26 of the Bears' 61 plays from scrimmage on offense -- 42.6 percent of the snaps. The team's other U tight end is Ben Braunecker, and he played 15 snaps (24.6 percent).
Burton caught two passes for five yards on three targets. Just having him back on the field as an added presence for the defense to monitor was important for the Bears.
Perhaps with a long week leading into Washington next Monday night, Burton can get closer to 100 percent.
The Bears were without second-year defensive lineman Bilal Nichols for the entire second half after he was ruled out with a right hand injury.
Nichols left the Bears' locker room after the game with his right hand in a cast. It was unclear Sunday the extent of the injury. Nagy may have more information when he meets reporters at Halas Hall on Monday, though it's possible Nichols will be undergoing further tests.
The Bears committed to a steady defensive line rotation to manage the altitude and heat in Denver. Without Nichols, who played only 11 snaps, the defense relied more on reserve lineman Nick Williams, who produced one of the team's two sacks of Flacco.
The Bears don't have a defensive lineman on the practice squad, so they could be forced to consider options around the league if Nichols is forced to miss an extended time.
When the Broncos needed to sustain drives, they used Joe Flacco as if he was Brock Osweiler. While there are jokes to be had in that statement, there's nothing funny about it to the Bears.
Denver coach Vic Fangio was on the sidelines as Chicago's defensive coordinator in Miami last October when the Dolphins beat the Bears by having Osweiler release the ball quickly. They set a first read out on a short route along the sidelines and distributed the football before the Bears' pass rush could have an effect.
Even the more limited quarterbacks like Flacco can find some success against the Bears with a quick release. It's something for Chicago defensive coordinator Chuck Pagano to keep in mind moving forward.
-- Bears defensive back Buster Skrine gave the Broncos a second life when he jumped offsides on their missed extra-point attempt with 31 seconds left. He explained that he jumped early because he was duped by Broncos long snapper Casey Kreiter, who subtly spun the ball on the turf before snapping. Skrine was looking to get a quick jump off the edge to block the kick.
-- The offsides penalty by Skrine overshadowed a strong performance from him. Pagano was plenty comfortable blitzing Skrine out of the nickel position, which created another wrinkle in his defense.
-- It was a small sample size, but Bears tight end Adam Shaheen looked more confident. He hauled in three passes for 24 yards and broke some tackles by asserting his size.
-- The atmosphere inside the newly-named Empower Field lived up to the hype. The entire building rumbled on each big play.
-- Broncos tackle Garett Bolles just got called for holding again.