Samsung Honda rider Lowes won a thrilling first race to close to within a point of Byrne.
The two duelled again in race two before, on the fourth lap, Lowes, closing in on his rival going into a left-hand turn, hit the back of Byrne's Rapid Solicitors Kawasaki at around 130mph.
Byrnes crashed out, suffering a gash and bruising to his left leg, but Lowes, having dropped back to fourth, battled back to retake the lead with four laps to go.
His joy was short-lived, though, as he was later excluded following a judicial after the incident for 'causing contact which resulted in an accident'.
The decision denied him what would have been a third consecutive winning double.
Lowes edged out Byrne by just 0.102 seconds to win the first race, with Tommy Bridewell (Milwaukee Yamaha) taking third place.
Milwaukee Yamaha's James Ellison was credited with the victory in race two, having crossed the line in second, with PJ Jacobsen (Tyco Suzuki) moving up to second and former three times British champion Ryuichi Kiyonari completing the podium.
The win moved Ellison 20 points behind Lowes in the standings, with Byrne a point further ahead.