Reynolds converted from provisional pole in the single-lap dash for pole, Reynolds running down long-time pacesetter Chaz Mostert.
The margin between Reynolds and Mostert was just 0.005s as the two Mustang drivers locked out the front row.
"It wasn't a bad lap," said Reynolds. "I knew our car was fast from qualifying before. The track is much slower so I just buckled in and had a crack, and it was alright.
"It was a bit messy here and there, not perfect, but good enough to be on pole."
While he missed out on pole, Mostert still made up four positions compared to qualifying in the Shootout.
James Golding matched his qualifying effort to grab third on the grid, the PremiAir Racing driver set to share the second row with Cam Waters.
Shane van Gisbergen qualified fifth ahead of Tim Slade, Broc Feeney, Jack Le Brocq and Todd Hazelwood, the earlier runners all affected by oil left on the circuit by a crash in the preceding Aussie Racing Cars race.
Courtney, meanwhile, became the first driver to inflict proper damage to a Gen3 car in the Shootout.
Running third, the Tickford driver tried to take a narrow line into Turn 8 to avoid the oil on the road.
However he got too narrow on entry, clipping the inside wall before firing the front of his Mustang into the outside wall.
"I'm fine; it's just frustrating," Courtney told Fox Sports.
"There is oil down there so I was trying to get in as close to the wall as I could to get around on the inside. But I got too close, clipped the wall on the inside and the show was over."
When asked if the car will be repaired for the race, Courtney added: "I don't know, I don't know how these new cars crash. We're the first ones to try it out. It's disappointing. All that hard work. We had good pace this morning."
The race kicks off 3:05pm local time.
