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".

The Norfolk and Suffolk NHS Trust eight-bed unit at Hellesdon Hospital is due to open to patients next year.
Mothers and their newborn babies will be able to stay together during psychiatric care, the trust said.
Referrals will come from Norfolk, Suffolk , Cambridgeshire and other parts of the country and the unit will work closely with local medical groups.
Mental health illnesses such as postnatal depression and severe anxiety will be treated as well as postpartum psychosis - a mental health condition which can occur in women who have just given birth and can cause hallucinations and delusions and can severely disrupt perception, thinking, emotions and behaviour.
Jessica Bannister, from Norwich, received mental health crisis treatment with Norfolk and Suffolk NHS Foundation Trust (NSFT) when she suffered this condition following the birth of her son, Albert, three years ago.
She then had to travel to Hackney, in London, for specialist inpatient treatment.
"The immediate care that I received from NSFT when I went into crisis was literally life-saving, offering an urgent short-term safe haven, and for that I will always be grateful.
"But there were no local facilities to treat my condition in a specialised environment," said the author and playwright.
"These units are incredible places - the humanity, love and support you receive is phenomenal. The dedication of the staff to your recovery and wellness, along with the love they give to your child, is fantastic."
She has written a drama documentary for BBC Radio 4 called Mama Courage, due to be broadcast on 12 May at 14:15 BST.

Arthur Howard, 74, and his 75-year-old wife Emma, from East Kilbride, South Lanarkshire, had the winning ticket for the Mega Friday draw on 29 January.
Mr Howard said he "went into complete shock" after phoning the claims line and hearing the words "Congratulations, you're a millionaire.
He now plans to trade in his taxi for a new Audi car.
Mr Howard said: "It has taken a while to sink in, I even had to phone the claim line twice just to make sure it was the real thing.
"When I first phoned and heard the words 'congratulations you're a millionaire' I went in to complete shock and told the call handler I would have to hang up and give her a call back."
Mr Howard added: "My youngest son came over to me as he was worried something was wrong as all the colour had drained from my face.
"I told him and he wouldn't believe me so we called the claim line back, putting it on loud speaker this time, and she said it again 'you are a millionaire'. It really was quite something."
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.
[NEXT_CONCEPT]
A £3m dedicated unit to help new mothers with serious mental health problems is to be set up in Norwich.
[NEXT_CONCEPT]
A Scottish couple are celebrating after winning £1m and all-expenses paid break to Dubai in a EuroMillions draw.