The rescue helicopter could not be used to reach her due to buffeting wind but a local man in a jet boat carried her to safety about 5pm.
It is thought the survivors were taken by ambulance to Wairarapa Hospital for observation.
The boating tragedy happened as Wairarapa police and search and rescue teams were scouring vast areas of the Tararua Ranges searching for a mountain runner missing since Saturday morning.
Alastair Shelton, 33, of Wellington, drove to Mount Holdsworth on Saturday, arriving at 7am, to go on a solo run.
He had arranged to meet family later but failed to turn up and has not been seen since.
The family notified police at around 3pm on Saturday and a search was mounted.
Mr Shelton is described as 6ft tall, of slim build, with short brown hair.
When last seen he was wearing a singlet, black shorts, lycra tights, bright green running shoes and he had a small backpack.
Senior Sergeant Carolyn Watson said the weather had hampered some aspects of the search.
She said 11 teams, from the Wairarapa, Palmerston North and Wellington, were searching for Mr Shelton.
Rescuers continued through Saturday night but a helicopter could not be used because of high winds and rain.
New teams were called in early yesterday and Senior Sergeant Watson said there was still doubts as to whether a helicopter could be used in the search.
Mr Shelton is said to be an experienced and fit mountain runner and has completed the Holdsworth-Jumbo Circuit track many times before.
"We're checking all of the track systems from Holdsworth Road and looking for any information on him," Mrs Watson said.