Rugby Australia quickly issued an apology Jones.
Jones later said that he had been abused by the same individual at halftime and fulltime of England's 21-17 victory which secured a 2-1 series win.
Former Australia international Matt Giteau, who played under Jones for the Wallabies, condemned the actions of the supporters.
Earlier in the series, Jones said he had been abused by Australian supporters at the Suncorp Stadium in Brisbane.
"I love coaching at Suncorp," Jones said. "That is a good experience. You have got 48,000 people all full of drink and all they want to see is their team win. When you turn them away, it is a great experience. A great feeling. I was coming out from the coaches' box and they all have their scarves on. When did Australians start wearing scarves? It is all the rage isn't it? They are not so smart now. Before the game they are coming up saying to me you are going to get belted tonight. Now they are a little bit more quiet. So that's good. I enjoy that."