It was a breakthrough for the 29 year old who won the time trial in 2013.
"I've been racing at the nationals for 10 years and come second to Gordon McCauley before which was a one-two-three-four in Subway days.
"To get the jersey now I feel like everything I've been working towards and building towards and putting in 10 years of hard work has definitely paid off and justification for sticking at it and nutting it out."
Local Christchurch rider Hamish Schreurs, who lives in Cashmere, claimed the under-23 honours, finishing seventh overall, from Auckland's Dion Smith and Te Awamutu's Hayden McCormick, last year's under-213 champion.
A strong group comprising McCormick, Christie, double Olympic medallist Westley Gough, Canterbury's Paul Odlin and 2013 national under-23 winner James Oram pushed out to a lead of three minutes 20 seconds after four laps but by lap eight the lead had shrunk to a minute.
They were caught three laps from the finish when Nelson's George Bennett, who will ride for World Tour LottoNL-Jumbo this year, bravely attacked up the hill as one of the world's leading climbers, joined by Avanti's Paddy Bevin.
The bunch came back together, as Orica GreenEDGE professional Sam Bewley loomed large, but it was Cooper's charge, backed by neo-pro Davison that proved the winning move.
After six years in Christchurch, where the event has gained new-found popularity with massive crowds on the Dyers Pass climb, the championships move to Napier for the next three years.