Footage posted on social media shows Jones being baited by a man wearing a Wallabies cap and holding a pint of beer.
The supporter points a finger at Jones as he walks on to the pitch and says “you’re a traitor” twice, provoking a furious reaction.
Jones stalks over to the stand and replies “come here and say it” three times, causing the surprised fan to back off, and is then ushered away by a member of the ground’s security staff.
The security guard can he heard saying to the fan “I have spoken to you before”.
It is understood that Jones, an Australian who coached the Wallabies from 2001 to 2005, was subjected to hostile abuse when walking to and from the coach’s box with the layout at the SCG meaning he had to pass through sections of the home crowd.
“Clowns think they have full go to abuse coaches,” Jones told the Sydney Morning Herald when asked about the incident.
The Rugby Football Union and Australian Rugby Union have been contacted for a response.
A week ago Jones spoke of how he took satisfaction from silencing Australia fans through England’s 25-17 victory in the second Test at Suncorp Stadium, although it is understood he did not receive the same level of abuse in Brisbane.
“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’s a great experience. A great feeling,” Jones said.
“I was coming out from the coaches’ box and they all have their scarves on. When did Australians start wearing scarves? It’s 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.”
Jones’ experience of abuse from fans is not limited to Australia, however.
On the 2018 tour to South Africa, he hit back at spectators at Ellis Park in a heated tunnel confrontation, standing his ground for 10 to 15 seconds before being taken away by players and staff.
Earlier that same year, he was physically and verbally abused by Scotland supporters in Manchester and when catching a train to London in the wake of a 25-15 defeat at Murrayfield.
The incidents were investigated by British transport police and Jones vowed to not use public transport again.
The bulk of England’s touring party return home on Sunday, although Jones and his assistants will spend next week at AFL team Melbourne Storm with a view to developing their coaching skills.
It comes at the end of a successful tour Down Under in which he masterminded a valuable series victory 14 months out from the next World Cup.
“The result is always important, but so is the development of the team. We are developing a team for the World Cup and it was crucial for us that we got it right,” Jones said.
“The results don’t always tell you that you got it right, contrary to what people think, but the development of the team has been outstanding.”