Robyn Malcolm had been photographing a pod of whales on a feeding frenzy 500km (310 miles) south of Sydney.
But she only realised she had taken the unusual picture when she went through the photos later, she told the Sydney Morning Herald.
Animal experts say that witnessing such a partnership is rare.
New South Wales National Parks and Wildlife whale expert Geoff Ross told the paper the coupling was very rare but he had heard of it happening once before.
"The only other time was a seal trying to get away from a killer whale. The seal hopped on the back of the pectoral fins of a humpback whale," he said.
Ms Malcolm insisted that the photo was not doctored.
"I'm positive, because I don't know how to use Photoshop. And I do still have it on the camera so I can prove it," she told the newspaper.
The meeting of seal and whale is the latest in a series of serendipitous animal piggyback rides which have been captured this year.
In March, amateur photographer Martin Le-May shot this picture of a weasel clinging on to the back of a woodpecker at Hornchurch Country Park in east London.
In June, a family walking in a forest in central Florida spotted this raccoon hitching a ride on the back of an alligator.
Mr Richard Jones told local television station WFTV that he "snapped a lucky picture right when the gator slipped into the water and before the raccoon jumped off and scurried away".
An Australian photographer has captured a rare moment of animal communion with a shot of a fur seal surfing a humpback whale off the New South Wales coast.