Lowes had ruled the timing charts from the early stages with continually-improving lap times but Australian Brookes leapt ahead of the WFR Honda man with 10 minutes remaining.
But a final best of one minute, 37.893 seconds put Lowes back ahead of Tyco Suzuki’s Brookes, who finished second-fastest at 0.282 seconds behind.
“I’m really enjoying riding here – the track suits my style,” reflected Lowes. “We are getting consistent lap times even though this is a new track for the team and we have all had to work hard.
"There is no reason why we cannot continue like this – we just have to stick in there. As for the Showdown and the title – I’m not thinking about either of them yet. My focus is simply to go out there and do my best.”
Shane Byrne (Rapid Solicitors Kawasaki), fastest in the opening session earlier in the day, was over half a second behind Lowes in third while Michael Laverty could only manage fourth on his Samsung Honda despite being among the front-runners throughout.
Hill’s crash late on at turn seven combined with stable-mate Noriyuki Haga’s session being cut short by a technical problem halfway through for a nightmare second free practice for the Swan Yamaha team.
Hill ultimately ended ninth-fastest regardless, with Ian Lowry also crashing unhurt and Jakub Smrz of Splitlath Redmond Racing rounding out the top five.
Hill said: “We headed out on used tyres just to get more feel on how the bike will be for race distance and to try and move forward with the overall package. It was a shame we didn't get a run at the end of the session on a new tyre because the crash ended our track time today; there is lots of time to be made around here with new grip.
"Overall though the package is feeling better and hopefully after our team meeting we can move forward again tomorrow for qualifying with my speed and setup.”
Free practice two times:
Alex Lowes (WFR Honda) 1:37.893s
Josh Brookes (Tyco Suzuki) +0.282s
Shane Byrne (Rapid Solicitors Kawasaki) +0.572s
Michael Laverty (Samsung Honda) +0.868s
Jakub Smrz (Splitlath Redmond Racing) +0.950s
Barry Burrell (Buildbase BMW) +1.071s
Patric Muff (Supersonic BMW) +1.182s
Luca Scassa (Padgetts Honda) +1.204s
Tommy Hill (Swan Yamaha) +1.261s
Chris Walker (Pr1mo Bournemouth Kawasaki) +1.370s