The big players, including time trial winner Jack Bauer, defending champion Jason Christie, Tour of Southland winner Aaron Gate, Gough, under-23 world mountain bike champion Sam Gaze and new World Tour rider Tom Scully.
They caught the leaders on the third lap and from that point attacks from Cooper, Smith and Christie up the climb were neutralised by the lead group on the flat.
Cooper, who won the national road title in Christchurch two years ago, made his move on the final climb.
He had a 17-second advantage going into the final flat lap and was surprisingly able to hold off the powerful chasers into the head wind over the first 5km and from there he was able to enjoy the run home.
Cooper finished 14 seconds clear of Christie, who followed his win last year with another impressive performance for the 26-year-old, who hopes the effort will help secure a spot in a professional team this year. Third went to Smith, also seeking a professional ride in 2017.
"Today was about keeping calm and waiting for the right move. I didn't have any teammates so I was forced to save energy and then unload at a certain point and hope that it stuck," said Cooper.
"You had to give respect for the World Tour and Pro Continental guys and so if you are able to hang around their wheels long enough you land in the right moves and get an easy sit in the peloton which was a key to the strategy today."
"I knew they were riding for a bunch kick and I can't sprint my way out of a wet paper bag so I needed to be solo. I had to roll the dice. There's no way I wanted to wait for the bunch kick and come 10th."
Pre-race favourite Bauer said he did not have the legs and felt pain on the first climb up Napier Hill.
"I knew I was in for a hard day from there. This course was tough, possibly tougher than Christchurch. I just did not have enough miles in the legs."
