The Red Rose pulled off a repeat of their tour triumph in 2016 by making it back-to-back series wins Down Under, beating the Wallabies 21-17 in the deciding Test on Saturday.
Jones was head coach of his country between 2001 and 2005, but has been in charge of England since 2015 following a spell with Japan.
After recovering from going 1-0 down in the series with a 30-28 loss in Perth, England won 25-17 in Brisbane last weekend before sealing the series in the decider.
Unsavoury scenes followed the match at the SCG, as two separate incidents emerged on social media that showed Australia fans baiting Jones, with one heading to the front of a stand to shout "You're a traitor" at the Tasmanian, to which the furious 62-year-old responded with, "What did you say? Come here and say it. Come here and say it."
A second video shows another fan also calling Jones a "traitor", which he again took exception to.
When asked for comment over the incident by the Sydney Morning Herald, Jones said: "Clowns think they have full go to abuse coaches."
It was not the first time in the series that Jones felt he had experienced abuse from home fans, suggesting he had faced similar jibes after the defeat in Perth.
"You have got 48,000 people all full of drink and all they want to see is their team win," he said. "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 [saying]: 'You are going to get belted tonight.' Now they are a little bit more quiet. So that's good. I enjoy that."