Rescuers, including a helicopter pilot using night vision equipment, feared the worst after a fruitless hour-long search around Pig and Pigeon Islands, near Glenorchy.
Dart River Jet's head boat driver, Geoff Baker, told the Otago Daily Times yesterday he heard a cry for help after he switched off his boat's engines.
"We just got lucky and heard a voice in the distance.''
Queenstown Harbourmaster Marty Black said the rescued couple, thought to be living in Queenstown but from overseas, were "incredibly lucky to be alive'' and owed their lives to the jet-boat crew.
Police say the couple could face charges.
Mr Black said despite the fact it is mid-winter, the couple set off to row to Pigeon Island in an inflatable boat with one lifejacket and two oars.
However, the boat took on water and when the pair tried to sit on the side it flipped, leaving them soaked and cold.
They used a cellphone to call police.
Mr Baker, colleague Jesse Mulgrew and paramedic Russell Varcoe combed Lake Wakatipu near Pig and Pigeon Islands, raking the lake with spotlights and cutting the boat's engine every kilometre to listen.
They eventually heard a cry for help about 600 metres away.
Mr Baker, who has been involved in several rescues, said: "Instinctively I knew the direction it came from.
"So we just headed up towards that about 300 metres and switched off again and didn't hear anything.
"But we were pretty sure we were on to something and we carried on another couple of hundred metres and there they were.''
The pair were cold and had "given up'' - they were making no attempt to save themselves, he said.
"She was in a pretty bad way - she'd been lying in the boat and the boat was full of water.''
Earlier, Mr Baker said searchers had become despondent and "we really thought it was a disaster''.
"It's very obvious to me that if we hadn't found them they were just going to shut down completely. They weren't close to shore, they weren't close to the island - and even if they were they weren't going to be able to warm themselves up.''
The rescuers were "very, very happy'' to find the couple, he said, noting there had been tragedies on the lake, previously.
Mr Baker said it was fortunate there was only "a small chop'' on Lake Wakatipu on Friday night.
St John Queenstown station manager Keith Raymond said the pair were moderately hypothermic when assessed on the shore.
They were warmed up and left in the care of the local police.
"They were really, really lucky, obviously - and very cold and a bit shaken, but they warmed up really quickly.''
A police statement issued from Wellington said police, Maritime NZ and local authorities could take action against those acting irresponsibly on the water.
"While police are glad they both made it back safe and sound, this incident could have ended very differently and could have been avoided had they been adequately prepared.''
