"Timaru was awesome. I got the hole-shot in the first and third moto and I was second at the start of moto two and followed my teammate for about three laps before I was able to get past.
"John was riding really well and it was a great day for Honda Shop Racing."
Behind the Honda duo some of Australia's leading riders battled for a podium spot with Luke Styke (KTM), Kirk Gibbs (KTM) and Kade Mosig (Yamaha) each managing a third position.
Cooper leads the series with 124 points, three ahead of Phillips going into the Rotorua round on March 8, which will be raced at the track built on the Phillips family property at Horohoro.
The battling Australians are led by Gibbs with 114 points from Mosig on 101.
Yamaha's Scott Columb (Queenstown), who had led after the opening round, crashed in practice, could only deliver a 12th and two 11th place results at Timaru and is now fifth overall on 99 points, while Taupo's Brad Groombridge (Suzuki) is sixth and his teammate Rhys Carter (Mt Maunganui) is 10th.
Australian Jay Wilson (Yamaha) extended his lead in the MX2 with three wins at Timaru and now holds a 20-point advantage over Takaka's Hamish Harwood (KTM), who posted a 3-2-3 scorecard last weekend.
Amberley's Micah McGoldrick (Honda) is third ahead of Rotorua's Scotty Canham (Kawasaki).
It was a day of mixed fortunes for Te Puke's Logan Blackburn (Suzuki) who was third fastest in qualifying and rode to fourth in the opening moto. He crashed out of the second moto, then put fifth place points on the board in the final race and runs eighth in the championship.
"I was in fourth battling with the second and third placed riders and the guy right in front crashed on the face of a jump," Blackburn said describing the crash.
"I hit his bike so hard my front wheel basically collapsed. The spokes were everywhere."
The bike was un-rideable and Blackburn suffered some bruises and grazes but returned for the third moto and battled to fifth.
The 125cc 2-stroke racing was dominated by Hamilton's Josiah Natzke (KTM), with a 1-1-1 record.