In a video message addressed to all Australians, the talk show host announced a Disney partnership with the Great Barrier Reef Foundation and the Great Barrier Reef Marine Park Authority to fund a program of wetland restoration and educational materials using Finding Dory characters.
"As you may know I'm a big fan of your beautiful, great, wonderful Great Barrier Reef which is home to my favourite fish, Dory," DeGeneres said.
"It's critical that we protect this amazing place. Help us help Dory 'just keep swimming'."
DeGeneres is also asking people to donate to native tree planting charity Greenfleet, which seeks to improve run-off to the reef.
Disney's environment and conservation senior vice president Beth Stevens said lots of Disney's films had a conservation message for children but that they also put their money where their characters were.
"Disney Conservation Fund has assisted many of the species seen in Finding Dory and worked to reverse the decline of threatened wildlife through scientific research, collaboration and community engagement," Stevens said.
"[This program] recognises the role the Great Barrier Reef played in inspiring the characters we know and love, and helps ensure the reef's beauty and diversity will continue to inspire generations to come."
An Australian group of scientists and conservationists had been calling on DeGeneres to speak out to dissuade people from buying wild-caught reef fish like their Disney characters.
The campaign Saving Nemo bred clown fish to meet demand with the hopes it would stop the wild-caught fish trade.
Flinders University Faculty of Science associate dean Karen Burke da Silva said that while DeGeneres didn't give a shoutout to Saving Nemo, her attention to the reef was invaluable.
"The reason we were keen to attract her attention is because her voice is loud around the world," Burke da Silva said.
"People listen to her and respect her views on conservation. For her to come out and say something positive about saving the reef is brilliant."
Burke da Silva said the Saving Nemo campaign, meanwhile, was also capturing hearts around the world.
"Right across the board all over the world people are wanting to help," Burke da Silva said.
"I got one particular message from a woman in a small town in Canada called Manitoba. Her daughter wanted to give a donation as a graduation gift to her friends. I had a graphic designer from the U.S. offering in-kind support.
"People the world over want to help and I think Australians recognise how important it is to protect the Great Barrier Reef."