The intrepid man was about three kilometres from Townshend Island, north of Rockhampton in Queensland, when the animal lunged at him on Wednesday.
He paddled furiously to land at the island, but was then stranded there by a combination of bad weather and tidal problems.
"He was very fortunate," a spokeswoman from the Australian Maritime Safety Authority, which coordinated the rescue, told AFP.
"It didn't pierce the kayak. He said he was running on adrenalin (to get to the island)."
Saltwater crocodiles have become more common in northern Australia since they were declared a protected species in 1971. They are estimated to kill an average of two people each year.
Several hundred are culled every year in Queensland and neighbouring Northern Territory to protect the public and livestock.
In May, a 46-year-old woman was presumed taken by a crocodile in far north Queensland when she disappeared after she went into shallow water at night.
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