A last-lap effort of two minutes 8.056 seconds saw the WFR Honda rider go just 0.004s faster than Luca Scassa of Padgetts Honda.
“We still have work to do, but already I am feeling confident that I challenge in these races,” said Lowes. “I am in the Showdown and I am not here to make up the numbers.”
Byrne was forced to watch from the sidelines after crashing the Rapid Solicitors Kawasaki almost immediately at the start of the session, but was largely unhurt after suffering just a bang to his left hand.
"It was a strange crash as when you are on the limit you can expect it, but it was only my second lap out," he said. "It flicked me up and I came back down on the bike and was heading into the gravel at a fair rate of knots so I had to bail out. I am ok though and ready for tomorrow."
Standings leader Brookes was third, two-tenths off the pace, after spending time in P1 early in the session, ahead of defending champion Tommy Hill.
“We are a bit down on track time here, but I am happy there is more to come from the bike but we have to push on,” said Hill.
Another title hopeful Michael Laverty was sixth on the Samsung Honda, whilst his team-mate Jon Kirkham ended the session prematurely with a technical problem.
Tommy Bridewell, the sixth rider in the Showdown, was down in 16th.
Brookes has 570 points followed by Byrne (568), Hill (548), Lowes (534), Laverty (532) and Bridewell (521).
1. Alex Lowes (WFR Honda) 2m08.056s
2. Luca Scassa (Padgetts Honda) +0.004s
3. Josh Brookes (Tyco Suzuki) +0.208s
4. Tommy Hill (Swan Yamaha) +0.605s
5. James Westmoreland (WFR Honda) +0.634s
6. Michael Laverty (Samsung Honda) +0.708s
7. Barry Burrell (Buildbase BMW) +1.169s
8. Jakub Smrz (Splitlath Redmond Aprilia) +1.170s
9. Robbin Harms (Doodson Motorsport Honda) +1.546s
10. Peter Hickman (Buildbase BMW) +1.561s