The 22-year-old from South Australia surprised himself more than anyone by powering away from a leading group of 15 in the final 2km to take the title.
Scotson, who will ride for BMC Racing this season, has got most of his best results on the track – with two world championship gold medals in the team pursuit event.
But he went into pure time trial mode to beat Simon Gerrans into second place, with Nathan Haas claiming third.
Scotson said: “I went all in with the one move, it was all or nothing.
“I was just so surprised I got around today but I really just have good support here that the team arranged.
“It’s really weird just racing in the national champions jersey in Europe this year is going to be a big jump. Maybe a bit of pressure I’m not sure how this season is going to go whether I can handle it in Europe so its time to lift my game.”
Although Gerrans missed out on his third national road title, he was full of praise for Scotson.
“What a great way for him to get his professional career started,” Gerrans said.
“I’m really happy for the young guy to get the win today, he really deserved it. He didn’t have any teammates so he raced a really smart race.”
In the women’s road race, time trial champion Katrin Garfoot made it a double by hunting down a break by Orica-Scott team-mate Amanda Spratt to take victory.
Spratt was going for her a hat-trick of titles, but was beaten by 35-year-old Queenslander Garfoot in a final sprint with Lucy Kennedy well adrift in third.
“It feels great. I’ve wanted to be here for a few years and I finally made it,” said Garfoot, who won the time trial last week.
“It feels definitely great and a double as well which was also a dream coming into it.
“It’s very special. It’s special because it’s such a rare thing to achieve this.”
Spratt might have expected to take victory after going off the front on lap seven, but her team-mate then reeled her in and had more strength and power in the last 100m.
“We were just talking to each other, going up the hill together. Our goal was to go up the hill together and ride together to the sprint,” Garfoot explained of her inter-team rivalry with Spratt.
Sam Jenner, 19, won the men’s Under-23 national road title with a superb breakway three laps from the finish, beating Alexander Porter into second place by 47 seconds.
“It wasn’t really the plan but it was a bit of a lull in the bunch and I thought it was time to go,” Jenner said of his attack.