Byrne again hit the front of the field on the opening lap of the race from Ellison and Alex Lowes, but the Milwaukee Yamaha rider edged ahead to take the lead from the reigning champion on the second lap.
Byrne looked set to make a move as Ellison had a moment out of Graham Hill Bend with three laps remaining and the Rapid Solicitors Kawasaki was forced to run on at Surtees to avoid a collision. The move dropped Byrne back to third after he rejoined the track behind Lowes as Ellison claimed the win.
Samsung Honda's Ryuichi Kiyonari had an improved second race as he returned to the top five and maintained his position ahead of Josh Brookes on the Tyco Suzuki and Jon Kirkham on the Buildbase BMW.
In the closing stages, Karl Harris was able to push ahead of Chris Walker after bouncing back from his crashes this morning.
James Westmoreland scored an impressive ninth place after his crash in race one and Keith Farmer completed the top 10.
Race two results
1. James Ellison (Milwaukee Yamaha)
2. Alex Lowes (Samsung Honda) +1.997s
3. Shane Byrne (Rapid Solicitors Kawasaki) +5.904s
4. Ryuichi Kiyonari (Samsung Honda) +11.507s
5. Josh Brookes (Tyco Suzuki) +15.974s
6. Jon Kirkham (Buildbase BMW) +21.280s
7. Karl Harris (PR Racing Kawasaki) +23.038s
8. Chris Walker (Quattro Plant Bournemouth Kawasaki) +23.390s
9. James Westmoreland (Buildbase BMW) +30.552s
10. Keith Farmer (Rapid Solicitors Kawasaki) +30.999s
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