"He got a kick in the calf," Henry said. "The doc's not sure how serious it is.
"He was certainly in a lot of pain after the game."
Carter, hailed as the world's leading fly-half after his 33-point performance in the Second Test against the British & Irish Lions, limped off midway through the second half.
But by then the damage had been done. It was his performance with the boot, and a virtuoso try by rookie scrum-half Piri Weepu, which kept New Zealand in the Cup contest after they trailed 13-0 in the opening 15 minutes.
The Canterbury Crusaders playmaker landed three penalties and two conversions to demoralise the Wallabies and revitalise their Tri-Nations campaign, which is heading for a showdown against South Africa at Eden Park, Auckland, in two weeks' time.
Henry was delighted with the manner in which the All Blacks fought their way back into the match, unlike last week's loss to the Springboks.
"A huge amount of character and heart was shown by the team after being down 13-0," Henry said.
"Australia played very well in the first 20 (minutes) but the guys climbed out of that and got better and better as the game went on and probably should have won by more. We are delighted."
Henry said the difference between the performances against the Wallabies and the Springboks was plain to see.
"We wanted to play (against Austalia)," he said.
"I think there was a bit of an aftermath from the Lions series and ruling off from that and starting again.
"I just don't think we ruled off and really got focused for the start of the Tri-Nations.
"That's the coach's fault.
"I did not perceive that to be an issue at the time (last Saturday) and we then got stomped on.
"We just didn't do what we should have done between the two campaigns."
All Blacks skipper Tana Umaga, who had been under an injury cloud all week, said the key to their victory was possession.
"We did show a lot more composure than last week," he said.
"Once we got the ball we had to hang on to it.
"It wasn't the perfect performance - we didn't make the most of our chances - but te ones we did take we are very happy with."
Umaga said the All Blacks' plan was to try to outmuscle the Wallabies.
"We wanted to get stuck in, we wanted to be physical," he said.