The 20-year-old, who won the national title in 2013, also claimed the top U23 prize with a winning margin of 1:10 minutes over Gaze who got his front wheel wedged in a tree during the final lap after both riders had gone clear of the field.
"I really wanted to get the jersey again," said Cooper. "I love wearing it overseas so I decided to focus on it (the elite race) a bit more, and it paid off.
"I just wanted to go out and hit most of the climbs hard. I did that but hit a flat spot mid-race and felt a bit sick. I came good though and for the last two laps of the race I felt really strong, although it was still really close and could have gone either way."
Last year Cooper, who rides for the Cooper rides for the Cannondale Factory Racing team, lost in a two man sprint against Gaze but there was no doubting who the 2015 champion would be when Cooper arrived at the finish on his own while Gaze untangled his bike from the tree.
"I was able to capitalise on a small fumble by Sam and stretched out a good advantage and pinned the ears back to the finish," Cooper added.
At the end of last season, Cannondale announced that it had extended Cooper's deal with the team for a further two season with the New Zealander focusing on world cup success this year with an eye on Rio 2016.