Cooper finished 3-1-1 in his three races on Sunday to top the standings for the day and Gibbs finished 1-4-4 for the runner-up position.
Phillips slipped down the series standings after recording a 4-7-6 in the three races.
Meanwhile, Tauranga's Ben Townley - making his only appearance in the series - earned Sunday's third podium spot with his 2-3-7 results.
When Australian visitor Jay Wilson arrived at the Rotorua track, he was a solid 20 points ahead of his nearest challenger for the MX2 (250cc) class honours, Takaka's Hamish Harwood.
At the end of the day, Wilson had boosted his advantage to 37 points over Harwood.
Wilson is clearly dominant in this class.
The 20-year-old from the Gold Coast has now won seven out of nine MX2 class races thus far.
In the smallest bike division, the 125cc class, Hamilton's defending champion Josiah Natzke scored another hat-trick of wins on Sunday, ballooning his advantage from 11 points over Taupo's Cohen Chase at the start of the day to 37 points over Ngatea's Ben Broad, who moved into second on the standings.
A crash at the start of the day's first 125cc race cost Chase dearly.
He managed to fight back from last position to finish 15th in that race, and backed that up by finishing third and second in the next two races, but it meant his title hopes suffered a huge hit.
Broad was a model of consistency, finishing 3-4-3, although he will need to step it up at the final round if he hopes to catch Natzke.
Chase is also breathing down his neck, sitting just one point behind.
The fourth and final round of the JT Racing-sponsored series is set for Harrisville, on the outskirts of Pukekohe, next weekend.
