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Gate, a key part of the track team for the Tokyo Olympics, edged WorldTour rider George Bennett by 0.7sec over the 44km test.
Michael Vink (St George Continental-Canterbury), the 2015 champion, was a further second back in a tightly fought individual test, although the elite trio had to give way to 20-year-old Finn Fisher-Black (Tasman) who won the under-23 honours in 54min 07.54sec, 9sec faster that Gate.
WorldTour professional Georgia Williams, who missed last year with injury, scored her third elite time trial title in four years in a strong performance, finishing 21sec faster than Tokyo-bound track rider Jaime Nielsen with Bronwyn MacGregor nearly 2min back.
"Something has always got in the way of the time trial. I wanted to give it a crack last year but my coaches decided it was too close to the track world champs.
"It was 2009 since I last rode it so this makes it all the more special," Gate said.
The win follows on from Gate’s victory in the Tour of Southland and the national championships.
Gate had a 20sec advantage on Bennett with a further 2sec to defending champion Hamish Bond at 14km but, with 9km remaining, the advantage was just 3sec.
He clung on to win in 54min 16.76sec with Bennett having to settle for runner-up for a second straight year just 0.74sec behind with Vink 0.9sec back in third and Bond fourth.
Fisher-Black, who won the under-23 time trial and road race last year, sealed the first of his double-double in emphatic fashion to win the under-23 honours by more than a minute from the Black Spoke Pro Cycling pair of Logan Currie and Dylan McCullough.
He heads to Europe on Monday where he will join the Jumbo-Visma Development team in a training camp in Valencia.
"I am scheduled to race on March 9 and pretty excited about what is ahead. There is George and myself for Sunday’s race.
"It is a good course, may be not as hilly as last year, but still with some good opportunities and some options to play with and George is on form."
Like Gate, Williams hammered the first half of the lumpy figure-eight course near Leamington, opening a gap of more than 30sec at the midway point and had more than enough petrol in the tank to claim her third time trial
"I am pretty happy with that.
"I was pretty committed to remain in Europe for the winter but I had a last-minute escape and such a good decision to come home for the summer. I am so lucky.
Henrietta Christie (Velo Project) dominated the women’s under-23 time trial, winning by more than 2min.