Judge Dawson permitted temporary interim name suppression until midnight so he could tell his family.
The man, dressed in a plaid shirt, had to sit in the dock due to a pre-existing medical condition. He was remanded in custody until his next appearance in June.
The maximum penalty for the abduction and grievous bodily harm charges is 14 years each and 10 years for the assault with intent to cause sexual violation.
After the arrest, Detective Senior Sergeant Kim Libby of Waitemata Police said they had spoken with the victim and she was "extremely relieved" to hear the news.
"This has been a traumatic experience for her and she is receiving ongoing support from her family, friends and police," Libby said.
"The investigation team has worked tirelessly over the past 14 days and we know this news will bring a great deal of relief to the Auckland community."
As part of a search warrant carried out at the Onehunga property, a 2008 Ford Mondeo has been seized and forensically examined.
Police also thanked the many members of the public who called the 0800 number and provided information during the past fortnight.
There had also been many businesses which assisted with the inquiry by promptly and proactively providing CCTV footage and police thanked them also.
