This result promptly handed the championship lead straight back to Vaughan.
Just four points now separate these two young men as they head to Taupo for the final round on March 31 and this class is one which will go down to the wire.
"I just couldn't get off the start line cleanly in the first two races today," Vaughan said.
"The pace is really hot and, if you don't get a good start, it's almost impossible to win.
"I only lost a little ground on Logan [Blackburn] ... he's closer to me by just one point ... so I just need to concentrate on doing everything right at the final round."
Meanwhile, riders of the distinctive blue and white bikes also finished on the podium in the other two championship categories as well.
While Vaughan and Blackburn were taking their Yamaha machines to battle for ascendancy in the 125cc class, the fight was on for Queenstown's Scotty Columb (JCR Yamaha Racing YZ250F) in the MX2 class and Scotland's Billy MacKenzie (JCR Yamaha Racing YZ450F) was in the hunt for top honours in the premier MX1 division.
An injured Columb finished an unaccustomed sixth overall in the MX2 class at Pukekohe - in a category where there is really little to separate the top eight or 10 riders - but it was enough to retain his overall championship lead.