Purdie started from third position and held ground at the front of the field, allowing Stewart to take over and race through to the lead.
Stewart led home the Ford Mustang of Blake Tracey/George Miedecke, with Jay Murray racing through to third place from outside the top 20 on the grid.
Glenn Walker finished in fourth position outright to win the Am Cup, holding off a late charge from the Chris Lillis/Nathan Callaghan Porsche.
Tony Quinn swapped the Silver-Am Cup lead in the closing laps with Dean Koutsoumidis to take the class win in 8th outright alongside Kiwi young gun Matt McCutcheon.
Lachlan Evennett led the field from pole position, relinquishing the lead to Aaron Cameron on the opening lap.
As Cameron ran away at the front in the opening laps, Caleb Paterson struggled to hold on to second place.
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Evennett was caught up in a mistake from Blake Dowdall, as the Mustang driver missed his braking point into Turn 1.
Light contact between both cars broke the steering in Evennett’s Toyota GR Supra, taking the car out of contention.
The sole safety car was drawn when Dowdall lost control through the Turn 11 and 12 complex, collecting Jensen Shearer.
As the field circulated under yellow, the majority of runners outside the top 10 elected to pit, with the lead group inexplicably staying out.
Those who stayed out included leader Aaron Cameron, who quipped there are “too many rules” in the category, citing confusion about the Mandatory Pit Stop (MPS) rules.
“I don’t think we’ve won this race now,” said Cameron.
“There’s too many rules in this category, so we’ve missed some rules, yeah, it sucks.
“I think at PI [Phillip Island] you couldn’t pit under safety car, and then maybe they sent out an amendment or something.
“I saw the rest of them peel in and we stayed out, that sucks.”
Lochie Dalton took over on the second safety car lap, emerging in 21st position.
Richard Craill confirmed on the broadcast that the rule states that the pit window will remain open under yellow flag at Race Control’s discretion.
Should a yellow flag fly at the start of the pit window, the safety car will remain out to allow the entire field to complete their pit stop.
Pit stop confusion saw almost a dozen cars penalised post-race at the Phillip Island season opener.
Miedecke emerged in the lead after the entire field had cycled through the pit lane, leading the field away at the restart.
Dalton carved back through the field on the laps following the restart, however was penalised late for a separate pit stop breach.
Stewart chased down Miedecke in the closing laps, running away for his first GT4 win on debut.
Silver Cup championship leaders Tom Hayman/Jett Murray were side-lined in the closing laps with steering damage, having started back in the pack.
GT4 Australia returns for Race 2 at The Bend on Sunday at 9:30am ACST.
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