The Tickford Ford driver was best of the green tyre runners at the back end of the session, a 1m12.629s vaulting him to the top right at the chequered flag.
The margins were tight, though, with the top four separated by less than a tenth and 22 of the 24 drivers within a second.
Van Gisbergen finished up just 0.05s behind Courtney with a late quali sim of his own, although he did need two bites at the cherry. He had gone purple in Sector 1 a lap earlier, but ran wide at Turn 6.
Bryce Fullwood was third quickest from Scott Pye, while Chaz Mostert, who'd been on top since the 10-minute mark, slipped back to fifth as more drivers switched to greens.
Andre Heimgartner, Anton De Pasquale, Todd Hazelwood, Scott McLaughlin and Nick Percat rounded out the Top 10.
David Reynolds spent half of the session stuck in the garage thanks to a misfire, eventually remedied with a coil pack change. He immediately jumped into the top five once on track, but slipped back to 11th after not running greens at the end.
Jamie Whincup didn't run a new tyre either and ended up 18th quickest.
|1||44|| James Courtney ||1'12.629|
|2||97|| Shane van Gisbergen ||1'12.686||0.056||0.056|
|3||2|| Bryce Fullwood ||1'12.699||0.070||0.013|
|4||20|| Scott Pye ||1'12.724||0.095||0.025|
|5||25|| Chaz Mostert ||1'12.784||0.154||0.059|
|6||7|| Andre Heimgartner ||1'12.893||0.264||0.109|
|7||99|| Anton De Pasquale ||1'12.915||0.286||0.021|
|8||14|| Todd Hazelwood ||1'12.940||0.310||0.024|
|9||17|| Scott McLaughlin ||1'12.979||0.350||0.039|
|10||8|| Nick Percat ||1'12.982||0.353||0.002|
|11||9|| David Reynolds ||1'13.026||0.397||0.044|
|12||6|| Cameron Waters ||1'13.097||0.468||0.071|
|13||55|| Jack Le Brocq ||1'13.128||0.498||0.030|
|14||3|| Macauley Jones ||1'13.164||0.534||0.036|
|15||22|| Chris Pither ||1'13.334||0.705||0.170|
|16||35|| Garry Jacobson ||1'13.340||0.711||0.006|
|17||5|| Lee Holdsworth ||1'13.366||0.737||0.025|
|18||88|| Jamie Whincup ||1'13.406||0.777||0.039|
|19||34|| Jake Kostecki ||1'13.407||0.778||0.001|
|20||12|| Fabian Coulthard ||1'13.420||0.791||0.013|
|21||19|| Alex Davison ||1'13.434||0.805||0.013|
|22||18|| Mark Winterbottom ||1'13.580||0.951||0.146|
|23||4|| Jack Smith ||1'13.641||1.012||0.061|
|24||15|| Rick Kelly ||1'13.751||1.122||0.110|
|View full results|