The 36-year-old closed out a classy victory by 0.191s to round out the weekend on a high following his earlier disappointment, with Ellison giving Shaun Muir's Milwaukee Yamaha team a deserved runner-up finish after he had crashed out in race one.
Lowes finished third without ever challenging the two men in front of him, while Brookes never figured after claiming his first victory of the season in race one, almost three seconds behind.
Kiyonari was fifth ahead of Buildbase BMW duo James Westmoreland and Jon Kirkham, with PJ Jacobsen eighth.
Quattro Plant Kawasaki's Chris Walker was a retirement on the fifth lap as the veteran endured a miserable weekend after a fall in the first race.
Padgett's Honda rider Jakub Smrz was caught out at Sheene Curve on lap 10 shortly after the safety car had left the course after the earlier incident involving Lee Costello at the same part of the circuit.