He was rushed to a waiting ambulance at Mangere Bridge and taken to Middlemore Hospital.
Earlier this afternoon hospital spokeswoman Lauren Young said the man was "doing well and stable in our Short Stay unit".
She has since confirmed the man has been discharged.
MetService said water temperatures in the Manukau Harbour last night were about 18C, which was relatively warm.
The overnight low in the area last night was 16C which was also warm although there had been winds of up to 40km/h, said meteorologist Lisa Murray.
"He's very lucky for someone who had to spend that much time in the water."
She said it was lucky the incident had occurred in Auckland, which had been very humid lately, as in places like Dunedin's south coast the water temperatures could drop much more dramatically at night.
Rod Frost, the skipper of the volunteer Papakura coastguard crew who found the man, said he was "a very lucky man".
"There were some rough conditions out in the Manukau Harbour, and although we were searching much of the night, we only spotted the man when our searchlights picked up the reflective strips on his lifejacket.
"The lifejacket kept him afloat throughout the night, and that undoubtedly saved his life."
However the man was unprepared, having only oars and a lifejacket and no forms of communication to signal if he got in trouble.
