McLaughlin closed on Pedersen and passed him, putting Murphy the necessary two places ahead of his title rival. His chances improved further when Pedersen lost time with a fast trip across the grass off turn one and lost a place to the Holden driven by Australian Tim Slade and Aucklander Richard Moore.
But then McLaughlin caught Murphy and put him under tremendous pressure, finally getting through to the lead with a clean move inside at the hairpin with 12 of the 70 laps to go.
Pedersen was now clearly struggling with his car and he fell back to fifth. He and Mostert did have the consolation of winning the endurance section of the championship; Murphy had earlier won the sprint series.
"We just didn't have the car to fight with, it's very simple really," a disappointed Pedersen said. "We were struggling with the tyres late in the race.
The final drama came as McLaughlin's car started streaming heavy smoke over the last two laps.
"I said [over the team radio] I'm not stopping!" McLaughlin, who also won the round overall, said. "It was the hub but the car was not too bad, it never really dropped off.
"It was good to get the first round win this season for the team; it's been an up and down season. To race with Murph at Pukekohe is pretty cool."
For the last part of the race Slade ran close behind Murphy but because Slade and Moore are part of the same M3 that Murphy drives for, it was clear that Slade was not going to try to pass and he finished third.
Shane Van Gisbergen had been in strong contention for the title after a big win in yesterday's shorter race, but early in today's first race the Ford's motor stopped and he was out of the meeting. He still took third in the championship.
Australian Lee Holdsworth blitzed away to a big lead over the first half of that race before handing over to Aucklander Tim Edgell, who piloted the Ford on to his second victory of the season.
McLaughlin and Moffat were second with Pedersen and Moffat third, which put Pedersen into the series lead as Murphy and Perkins were fifth, unhappy with the balance of their car.