Johnson brought the #114 McLaren home, keeping a cool head after inheriting the lead from Exton and leading the entire second half of the race, earning the pair their maiden GT4 win.
Blake Tracey/George Miedecke (#35 Ford Mustang) came home in second, with Sam Paley/Jack Wallis (#62 Mustang) rounding out the top three.
Aaron Cameron/Lochie Dalton (#27 Mustang) leapt up the order in the pit stop cycle to finish fourth, ahead of Multispares Racing teammates Cam McLeod/Mason Harvey (#227 Mustang).
Blake Purdie and Exton got away to an even start on the front row, however a strong push from Tom Hayman on the second row allowed the pole-sitter to hold the lead into the first corner.
Exton held on around the outside of Turn 1 to slot into second spot ahead of Hayman.
Purdie set about building a gap in the opening laps as the field settled into a rhythm.
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Silver-Am race winner at Queensland Raceway Caleb Paterson was forced to pit in the early laps from the top 10.
The #46 Porsche Cayman had suffered from overheating, which forced the car into limp mode.
American Ford Racing junior Paley was in the thick of the battle with fellow Mustang competitors Tracey and McLeod in the opening laps.
Tracey held off the charge, while Paley was then forced to drive on the defensive from McLeod.
In the lead up to the pit stop window, Exton began to close in on Purdie, bringing Hayman into the fight as well after several laps.
When Purdie handed over to Supercars rookie Jobe Stewart, the Audi was compromised in traffic as Exton continued to run long at the front.
Once the pit stop cycle was complete, Stewart was left circulating in eighth.
Johnson took control of the #114 McLaren, and emerged after the compulsory pit stop still in the race lead.
Despite having an additional 10 seconds of pit stop compensation time from the previous round, Mason Harvey took over from McLeod and continued to circulate in the top five.
Miedecke vaulted to second place once the pit stops had cycled through, and set about chasing down the leader in the laps following.
Johnson relinquished some of his advantage in the first few minutes after taking over, but built a steady gap over Miedecke in the run to the finish.
Hayman and Jett Murray (#25 McLaren) held on to sixth place, ahead of Purdie and Stewart (#48 Audi).
Daniel Frougas/Chris White (#9 Toyota Supra) finished eighth ahead of Silver-Am Cup winners Lachlan Evennett/Andrew Torti (#88 Supra).
Dean Campbell/Cody Burcher (#118 Mustang) rounded out the top 10 in their return to the series.
Jarrod Keyte (#21 Mustang) took the Am Cup win in 17th position outright.
Monochrome GT4 Australia returns for a second and final one-hour race on Sunday at 11:30am ACST.
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