Jones is facing disciplinary action from the governing body of the Tri Nations, Sanzar, after publicly criticising referee Mark Goddard in the post-match press conference.
Jones highlighted decisions made about the scrum, saying: "We're saying the scrum is a contest, and so the stronger scrum gets penalised. It just doesn't make sense."
However, Fisher defended the performance of his side's scrum and said he believed there was little for Jones to gripe about.
"I don't think he's got any real cause to complain," he said.
"I think they had us under a little bit of pressure, there's no doubt, but I think we had them under pressure as well.
"I think they turned over two of ours, and I think we affected three or four of their deliveries and got us side up, but I still think if you look at whether they scrummaged legally, is Greg Holmes allowed to scrummage with his left hand on the ground at engagement? No, he's not.
"And if you look at Rodney Blake's scrummaging on his right knee and at the height he was attempting to scrummage, again, you just can't do that. I don't think they were that dominant over us."
Former Wallabies hooker and current forward coach Michael Foley has been working with the Brumbies pack during the week to train its forwards ahead of the World Cup in September this year � a move that Fisher has applauded.
"The Wallabies are going to all the set-piece sessions that they can, of the provincial sides, to look at the development of particularly the front-row players, and to work with the Super 14 coaches to try to enhance our forward play, so it's invaluable having him down here," Fisher said.