On home ground, the Norwegian rider went clear over the top of the Kinnshaugen climb before linking up with Saxo-Tinkoff’s Sergio Paulinho on the trip back to the centre of Lillehammer.
A dozen cyclists attempted to reel in the duo, but despite getting close the gap began to stabilise in the latter stages.
From there, Boasson Hagen stepped up another gear and completed a popular solo victory by 11 seconds.
Boasson Hagen said after the win: "It's an amazing feeling to win here again. The team did a really good job today in controlling things from the start.
"After they'd done all the work other teams began attacking me and I decided to go by myself on the way to the finish.
“I'd planned to do that this morning and I wanted to try and either arrive alone or have someone to ride with. Everything went to plan."
The Norwegian national champion took both the yellow leader’s jersey and the green points leader’s jersey with the stage win.
Alexander Kristoff, the overnight race leader, lost contact with the pace-setters on Saturday after a brisk initial pace thanks mostly to Boasson Hagen’s Sky team.