With Byrne breathing down his neck, Lowes was defending his lines on the last lap and never put a foot wrong as he looked on course to extend his championship lead.
However, Byrne held a tighter line through Woodcote to mug Lowes on the line by 0.012s, moving back to the series summit ahead of his home round at Brands on October 20.
Bridewell was three seconds behind in third, with Ellison passing Brookes on the final lap for fourth. Series rookie Jacobsen was sixth.
Jon Kirkham took seventh on the Buildbase BMW ahead of Matteo Baiocco on the Rapido Sport Ducati.
James Westmoreland (Buildbase BMW) and Jakub Smrz (Padgett's Honda) were the top ten.
Noriyuki Haga finished 14th on the Rapid Solicitors Kawasaki ahead of Freddy Foray on the Samsung Honda.
to view Race 2 results