Playmaker Cooper sent a scare through the Wallabies' camp when he was unable to take his place in Friday's captain's run at St Joseph's college.
And, while he claimed he would have played no matter what his condition, he revealed he initially feared the illness might cost him a Test cap.
"I wouldn't say I was a chance of missing, you're going to play a Test match every opportunity you get," Cooper said.
"I'm sure that no matter how sick you are you're going to get up for a Test match.
"I was a bit nervous, but I'm just glad that my body got back in shape and I was able to run around out there with my team-mates."
The 23-year-old appeared in perfect health last night as the Springboks were unable to cope with his sublime footwork slick passing game.
He had a hand in three of his side's five tries and was just pipped for man-of-the-match honours by half-back Will Genia.
But Cooper was not getting too carried away after the win, declaring there was still significant improvement to be made.
"Rugby's never very much a perfect game so I'm very happy with the efforts of the boys and the way that everyone just kept backing up," he said.
"We could have scored a few more tries, but also there were few that we did make - like that try that James O'Connor scored (early in the second half) - that could have been a knock on but the skill that James showed there to scoop that ball up and score was just great skill."
Cooper combined to great effect with full-back Kurtley Beale and right winger O'Connor.
"It's really good to be playing with those boys again," he said.
"The skill that they show, and we're great mates away from the field and I think that shows out on the field.
"The amount of time that we spend together gives us a good understanding of where each other are out on the field and we're just having fun."
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