The chase through the pack track saw Cooper almost two seconds a lap faster than his rivals as he powered back from 17th place at the end of lap one. He was seventh after three laps and then picked up more positions with the crucial pass on Scott Columb to gain fourth place being completed with two laps remaining.
"I knew I had to be fifth but when Rhys got into the lead I had to pass Scotty to be fourth," said Cooper.
"It feels a bit strange to crash twice and still be able to win."
Carter grabbed his second win of the day ahead of Groombridge while Coppins made sure of third overall with a third placing.
It was the opening race that put Carter behind on the scorecard.
"I thought I had a good start procedure worked out but it just spun off the line and then I got cut off. I was almost last away from the first corner," Carter said, who is riding for the new Tauranga-based 3Twenty3 Racing squad.
"My speed is good and my fitness is okay. The best thing is I just settled into the groove and rode better as the day went on.
"The track started out really smooth but it was brutal by the end of the day. The holes got really deep."
The five moto format was also used for the 38-strong MX2 (250cc) contest and saw Hamilton's Josiah Natzke and Hamish Harwood (Takaka) battle out the Summercross title on KTM machines.
Natzke secured the win by a five-point margin - his three wins, one second and a third placing just a shade better than Harwood's scorecard of two wins, two seconds and a third. Reporoa's Hadleigh Knight (Husqvarna), Taupo's Cohen Chase (Yamaha) and Aucklander Ethan Martens (Yamaha) completed the top-five.
The Youth MX category (15-21 years) was won by Ohaupo's Trent Collins (Honda) who followed up a Junior 250cc class win on Sunday to lead home Taupo's Wyatt Chase (Yamaha).
Josh Coppins won the 35+ category and Hamilton's Darryll King cleaned up the 45+ age group.
Tauranga sisters Jessie and Casey Waterhouse headed the near capacity Women's MX field, Casey winning the opening moto but Jessie then posting two wins to clinch the Summercross title.