Byrne, the overall winner in 2003 and 2008, missed rounds eight and nine after suffering a shoulder injury but was back out for round 10 as the top six entered the Showdown for the title.
In a dramatic first race that saw Championship leader Tommy Hill suffer an unfortunate crash before the green light came on, Byrne showed his class to take victory.
It was a historic win as well with the BSB paddock racing at the famous Assen circuit for the first time ever however the Rapid Solicitors Kawasaki rider still has it all to do to win a third title.
Fellow title fighters Josh Brookes and Alex Lowes diced for second with the Australian Tyco Suzuki rider winning that battle, while Tommy Bridewell overtook Michael Laverty late on for sixth.
On a weekend full of expected excitement, there was drama before the paddock even lined up on the grid for race and it was bad news for Hill.
According to Hill, he was sent tumbling over the handle bars after a mechanic from another team ran out in front of him and clipped his break lever.
With Hill absent for the start, Laverty raced into the lead for the first lap however Byrne was to pass him on lap two, the dicing between the two to become the theme of the early part of the race.
While Laverty and Byrne were doing so early on, out came Hill, despite an apparent crack in his chassis, seemingly testing his Swan Yamaha bike in a bid to compete properly in race two.
The grid also lost two riders early on with Tristan Palmer and Victor Cox crashing out while Hill’s foray did not last long and he was soon back in the pits looking glum.
At the front Laverty overtook Byrne by the halfway stage only for the Rapid Solicitors Kawasaki rider to return the favour after which he eased away from his Showdown rival.
Team WFR Honda rider Lowes pushed himself up into second and became the rider most likely to challenge Byrne for top honours at that stage while Laverty and Josh Brookes battled for third.
Byrne eased to victory as Brookes shrugged off Laverty and then roared past Lowes to finish second to his third with Laverty succumbing late on to Lucas Scassa, Noriyuki Haga and Bridewell.
Race one results
1. Shane Byrne (Rapid Solicitors Kawasaki)
2. Josh Brookes (Tyco Suzuki) +4.731s
3. Alex Lowes (WFR Honda) +4.881s
4. Luca Scassa (Padgetts Honda) +9.327s
5. Noriyuki Haga (Swan Yamaha) +10.024s
6. Tommy Bridewell (Supersonic BMW) +11.026s
7. Michael Laverty (Samsung Honda) +11.538s
8. James Westmoreland (WFR Honda) +17.160s
9. Stuart Easton (Rapid Solicitors Kawasaki) +23.137s
10. Robin Harms (Doodson Motorsport Honda) +23.292s
- Michael Laverty
- Josh Brookes
- Tommy Hill