As Scotson slowed down to celebrate over the line, Simon Gerrans (Orica-Scott) sprinted desperately, finishing closely behind to claim silver while Nathan Haas (Dimension Data) rounded out the podium.
In his first race for BMC, the 22-year-old Scotson said he felt no pressure from the team.
"I went all in for the one move. That's how I race," Scotson said. "I was feeling really good on the climb. I stayed patient.
"I thought if I get there in the end, I'm going to whack it."
"No way did I think I'd get around 18 laps today with the training load I'd done. There was no pressure. I wanted to have a crack and enjoy it. I asked the mechanic to put on a 54 chain ring and stuck with that tactic."
As it happened
After 100km and a flurry of early attacks, the break of the day had established a lead of two minutes and 53 seconds.
The strong breakaway comprised Jay McCarthy (Bora-Hansgrohe), Lachlan Morton (Dimension Data) Luke Durbridge (Orica-Scott), Pat Lane (IsoWhey Sports SwissWellness), Caleb Ewan (Orica-Scott), Neil Van Der Ploeg, (IsoWhey Sports SwissWellness), Cameron Meyer, and Robbie Hucker (IsoWhey Sports SwissWellness).
With 30km still to race and after a lap lacking cooperation, the gap to the peloton dropped significantly to just one minute and 19 seconds.
The catch was made by the main bunch with 18.6km remaining and a larger group of 17 riders formed that now contained Scotson, Gerrans, Brendan Canty (Cannondale-Drapac) and Haas.
Canty attacked soon after the catch was made on the climb, building a 40-second gap to the peloton on Durbridge his nearest chaser, 12 seconds behind and held this lead until the next time around the start/finish line.
Unaware one lap still remained, Canty began to celebrate, his body language visibly changing once the bell rang. He was caught soon after by Durbridge. After several attacks back in the main bunch, it finally made the catch with six kilometres to go.
But the day belonged to the talented Scotson, who had no BMC team-mates in the race.
He was part of the team pursuit squad that won last year's world title, but he missed out on Olympic selection.
He won the under-23 individual time trial bronze medal late last year at the world road championships.
Scotson also won the under-23 time trial and road race at the 2015 nationals.
Gerrans, who revealed he was sick over Christmas, was disappointed not to win his third national title - but paid rich tribute to Scotson.
"It's disappointing when it's so close," he said.
"What a great way for him to get his professional career started - I'm happy for a young guy to get the win there today, he really deserved it."
Haas likewise tipped his hat to the winner.
"Obviously Miles was an exceptional winner today, this course has no gifts and it takes no prisoners," he said.