The rugby league convert received a yellow card after clattering into Halfpenny while the Welshman was catching the ball in the air in the 60th minute of Australia's 25-23 victory in Melbourne.
Vuna immediately made an apologetic gesture to Halfpenny, who had landed on his head, and the judicial officer who reviewed the tackle after the winger's citing decided there were mitigating factors "including a lack of intent", the Australian Rugby Union said.
Vuna, who came in to the Australia side to make his debut in the first Test only after Joe Tomane suffered an ankle injury in training, might not start on Saturday in any case.
Kurtley Beale, who missed Australia's victories in the first two Tests with a shoulder injury, is close to full fitness and could be available for the match at the Sydney Football Stadium.
Wallabies coach Robbie Deans had indicated he would pick Beale at full-back if he was fit, meaning a likely move to the wing for the versatile Adam Ashley-Cooper.
Deans will name his side on Tuesday.