Inspired by debutant Herschel Jantjies in Johannesburg, South Africa cruised to a 35-17 win at Ellis Park.
South Africa capitalised on Taniela Tupou's's yellow card to run away with the game in the second half.
While Hooper was happy with Australia's attacking performance in the first half, he conceded it must learn its lessons from the defeat, with New Zealand and Argentina still to come before the Rugby World Cup in Japan.
"South Africa controlled the second half so well," Hooper said.
"We had a few opportunities in the first half which would have created a different picture but pat on the back to the South African team who controlled the ball and took advantage of the yellow card and took the match away.
"Our attack in the first half was world-class. We showed a lot of different pictures but the reality is those things didn't happen and we were left with them doubling our points. There's a lot to look at."
Springboks coach Rassie Erasmus, however, was not pleased with how his side performed despite the convincing victory.
"A few guys certainly put their hands up for World Cup selection, but from a team performance perspective, this isn't how we want to play," he said.