A 75th-minute try from replacement fly-half Mat Rogers, and a conversion from Stirling Mortlock, sealed a 20-18 victory for the Wallabies despite a lacklustre performance on Saturday.
Apart from their record 49-0 win against the Springboks in Brisbane, Australia's half-backs have failed to shine in this year's competition, with scrum-half George Gregan and fly-half Stephen Larkham under increasing pressure.
Jones told radio station 2KY Australia's veterans were becoming a liability and changes need to be looked at if the Wallabies are to be a threat at the World Cup next year.
"You keep on getting the good games here and there from the older players ... but at the end of the day those good games get less and less," Jones said.
"If you look at the performances on Saturday, one of the things that probably stood out watching, it was the lack of energy in the side.
"Whether replacing some of the senior players, or making changes to other people, there definitely needs to be changes in the team."
Jones believes if changes are to be made, they need to happen in the near future to give the side plenty of time to prepare for the World Cup in France.
"I would not rule George out straight away, but there has to be another option," he said.
"Josh Holmes is certainly an option and I think the other one they should definitely look at is Matt Giteau - he is an outstanding half-back."
The new Queensland Reds coach believes it is crucial for the Wallabies to get the half-back combination perfect if they are to challenge New Zealand in the near future.
He said: "What you have got to do out of that nine and 10 position now is get a good vibrant 80 minutes out of it, and that has got to be the key to selection."