"We didn't want to lose him to the sin bin when he did, but he was trying to make a try-saving tackle and didn't intentionally go for a head-high tackle," Cheika said.
"I thought he put us in good position early on and made some good plays and led us around the park well, until he had to leave the field."
Cooper made a few handling errors and was hounded by the 48,457-strong crowd for each one, but did as much as a five-eighth could behind a beaten pack against the red-hot world champions.
Cooper said he was happy with the majority of his performance.
"I feel that I did well," Cooper told reporters after the match.
"I did the job I needed to do in terms of controlling the team around while I was out there.
"I was disappointed with not being able to stay out there for the whole game but that's the way it's gone."
Cooper said the jeers of the crowd didn't bother him.
"It's professional sport. The crowd hasn't got anything to do with it," he said.
"My mindset had blocked that out. I'm accustomed to training to that now. I expect that."
"It was that little period after half-time that I felt we just made some poor decisions. That led into the sin bin, and boom," Cheika said.
"The key issue is that we didn't improve from last week's performance and the opposition did.
"The margins are like that. You go away from home and that's what happens."
Aside from an encouraging opening period, the Wallabies had no answers once the irresistible All Blacks found their groove.
For New Zealand, it was an emphatic response to last week's loss in Sydney and the perfect way to farewell six veteran stars - among them skipper Richie McCaw and Dan Carter - who were likely playing their last Tests on home soil.
McCaw was playing in his 142nd Test, which makes him the most capped international rugby player in history.
"Sport's an interesting thing, isn't it. One week you're a mug, everyone's saying you should be out of the team," All Blacks coach Steve Hansen said.
"The next everyone's writing them up as heroes.
"Whilst it hurts and it sucks to lose, it's just another good reminder that occasionally you have to do it to go bone-deep and find out about yourself."
The result adds another year to Australia's long wait for the Bledisloe Cup and continues their miserable record at Eden Park, where they have not won since 1986.
- AAP