The 22-year-old Gaze went on a late charge to outsprint Cooper to win men's cross-country gold after he was forced to stop with a mechanical in the technical zone.
South African Alan Hatherly while an under the weather Dan McConnell (AUS) finished sixth at the end of the seven-lap, 4.5km course.
"I went in with one goal and one goal only and I'm honoured I could take it out," Gaze said. "I've also got racing on Saturday with the men's road race so I wanted to conserve best as I can and make up where I could."
However, Gaze took issue with Cooper's tactics as he entered the technical zone and flashed his middle finger as his countryman rode away.
"There's good sportsmanship and there's not and I felt like that wasn't there today. It's a bit of a shame really," Gaze said immediately after the race.
— 7CommGames (@7CommGames) April 12, 2018
Cooper, who was five metres ahead of Gaze heading into the final lap, disputed Gaze's version of events, saying he was under no obligation to slow down and couldn't see why Gaze had stopped.
"I didn't know if he was feeling unwell or something had gone drastically wrong - it's not my job to sit around and wait at that point," Cooper said. "I can't think of a situation where anyone would sit and wait."
Gaze later released a statement apologising for his behaviour and said he had also apologised to Cooper.
"I'm a competitive guy and when I had that issue with my bike I thought my dream was over," Gaze said in a statement.
"I am really embarrassed for how I acted and how the impact of how special of a day it was for New Zealand cycling was tainted by my actions."