Morton's breakaway mates Andrew Talansky (Cannondale-Drapac) and Adrien Costa (Axeon Hagens Berman) fought for the podium scraps, with Costa taking second and the young leader's jersey.
The Australian launched an attack from a decimated peloton on the punishing category one Mt Nebo climb. He was soon joined by Talansky and Costa, the trio increasing their advantage on the 35km descent into Payson.
— The Tour of Utah (@TourofUtah) August 3, 2016
Morton won an identical stage in Payson in 2013, his first win as a professional.
"I won this stage last time. I knew it really well. It all worked out pretty much how we wanted," the Jelly Belly rider said in the post-stage press conference.
"I felt pretty good, and when it's a small group like that if you hit them hard enough they hesitate for a second and you've got a small gap, and then that can be it.
"It was also the only time in the last 30km that we didn't have a headwind, so you've got to take advantage of that. If I had left it to a sprint, it usually doesn't end up very well for me."
Morton said the team could leave the Tour happy with this win.
"The Tour could end today and we'd be pretty happy, we kicked a big goal."
A group of six riders attacked early on in the stage the enjoying a maximum advantage of four minutes but split after the final intermediate sprint, the last rider, Simon Pellaud (IAM) breaking on the lower slopes of Mt Nebo.
See the stage replay on the Tour of Utah Tracker.