Retired accountant Graham McCready asked Judge Ema Aitken to stop Mr Jones appearing on Banks' behalf.
McCready alleged Mr Jones had attacked his character and misled the court over his ability to travel from Wellington.
He also told the court that he had lodged a complaint with the Law Society.
Judge Aitken dismissed the application as a "very long bow".
"That is a very serious allegation to be made, in particular to a Queens Counsel."
She said there had been no finding from the Law Society and lawyers facing complaints regularly appeared in court.
Mr Jones described McCready's intentions as "misguided at best".
"There has been no impropriety of any kind and Mr McCready is simply attempting to use the law to his own advantage ... There is no substance whatsoever to any of his allegations."
Outside court, Mr Jones dismissed McCready's application as "complete and utter rubbish".
A spokesman for the Law Society said of the 1625 complaints lodged last year, 86 per cent did not require further investigation.
Banks' case will be back in court in July but he has been excused from appearing.
Outside court, McCready said he would be appealing against Judge Aitken's decision to allow Mr Jones to appear.
He said Mr Jones had called into question his character by mentioning his convictions.
McCready went on to confirm that he had been convicted, referring to his being found guilty of filing false tax returns in 2009, and blackmail in April.
Banks told waiting reporters that "it was not the end but the end is in sight".
Banks is before the court to answer allegations that he received money from Dotcom and SkyCity during his run for the Auckland mayoralty in 2010 but declared them as anonymous.
McCready filed court documents to bring a private prosecution against Banks after police determined they could not lay a charge because it was outside the six-month time limit for summary charges to be laid.
In a decision released last month, Judge Ian Mill said Banks should answer the allegations that relate to two $25,000 donations from Dotcom and his company Megastuff Ltd. A third donation of $15,000 from SkyCity Casino is also included in the allegation.
He said material supplied by Mr McCready showed there were a number of people who could comment on what Banks knew and when.
McCready took assault proceedings against then Labour Cabinet minister Trevor Mallard in 2009 after the MP's scrap with National MP Tau Henare in the lobby of Parliament.
Mr Mallard pleaded guilty to fighting in public and paid a $500 fine.
