Wallabies officials said he was awake but concussed.
They lost Barnes 10 minutes earlier with a chest injury while Samo suffered a shoulder injury early in the second half.
The Australians, who were looking to extend their winning streak over South Africa to six and win for the first time at Loftus, were never in the hunt.
They trailed 14-3 at half-time, which could have been much greater but for the home side missing four penalty kicks while they had two tries disallowed by the television match official.
Wallabies five-eighth Kurtley Beale failed to spark their attack with his team smothered by hungry Springboks defence.
Their kicking game was again poor, while they missed too many tackles in a disappointing outing all around which will again turn up the pressure on coach Robbie Deans.
While Kirchner's foot touched the line when he was tackled by Ashley-Cooper, he had already opened the scoring at the 20 minute mark when the Springboks sent the ball wide to the charging fullback.
Francois Louw also barrelled across the line while the Wallabies were temporarily down to 14 players with prop James Slipper yellow-carded for a professional foul.
Mike Harris scored the Wallabies only try of the match.
South Africa claimed the first four-try bonus point of the Rugby Championship.
- AAP