Chardon, 68, was driven to the Brisbane police watch-house in an unmarked government vehicle on Friday morning.
He appeared in the Brisbane Magistrates Court shortly after noon on one count of murder and was remanded in custody.
The matter was set down to return to court for a committal mention on August 29.
Indonesian-born Novy, 34, was last seen at a Coomera service station in February 2013 and her car was found at a Nerang train station a few days later.
But despite extensive searches and a $250,000 reward for information, her body has never been found.
Chardon has been interviewed several times by police over his wife’s disappearance but has repeatedly denied any involvement in her alleged murder.
The two were married for 11 years but their relationship had broken down by the time of her disappearance and they were preparing to divorce.
Two days after Novy’s disappearance, Chardon flew to Indonesia with their children, then aged nine and seven, on what he said was a prearranged business trip.
In media interviews days after she vanished, he claimed Novy had “done this sort of thing before” and appealed for her to “get your stupid bloody a*** home”.
Police say Gold Coast detectives and officers from the State Crime Command Homicide Investigation Squad had been relentlessly pursuing justice for Novy since she went missing.
“Today we see the culmination of the hard work done by all officers involved in this investigation,” Detective Superintendent Dave Hutchinson said.
“There have been thousands of hours spent by investigators, intelligence officers and forensic specialists to try and bring closure to Mrs Chardon’s loved ones with the charging of a man today.”
Outside court Chardon’s lawyer, Craig Newport, said his client was holding up well.
Asked if Chardon was surprised by the accusations, Mr Newport said: “No, and he’ll be defending those charges.”