The probe has detected traces of molecular hydrogen (H2) in icy plumes spewing from fissures on the surface of Enceladus.
The discovery, reported today in the journal Science, indicates the Saturnian moon's oceans contain conditions critical to fuelling life.
Study co-author Hunter Waite, the program director of mass spectrometry studies at the South West Research Institute, said the implications of finding hydrogen were "pretty amazing".
"This boosts Enceladus to the top of the list of places in the solar system, apart from Earth, that we would consider to be habitable," he said.
In 2015, analysis of hundreds of images taken by Cassini indicated Enceladus has a global ocean lying between its hard rocky core and icy surface.
To explore the composition of the ocean, NASA scientists sent the spacecraft on a daring deep dive through plumes of icy material that spew from the moon's south pole.
Past fly-bys of the small moon indicated the plumes contained a mix of gases, water vapour, carbon dioxide and organic materials.
But the latest mission provided the first evidence the ocean also contains hydrogen.
"The problem early on was it [Cassini] was flying by really fast and these instruments had never been designed for this job," he said.
"We realised the only way we were going to do this was to operate the instrument in a very different fashion."
What does the discovery tell us?
Dr Waite said the hydrogen in the plumes was most likely produced by hydrothermal reactions between hot rocks and the water in the ocean.
"We went through an inventory of the different ways you could create the hydrogen you saw, and that was the most obvious source," he said.
The reaction charges the hot water with the chemicals necessary for microbial life to survive.
This process, known as methanogensis, happens around hydrothermal vents deep on the floor of the Earth's oceans.
"Hydrothermal systems on Earth use hydrogen as a food source … to create methane," he said.
Dr Waite said the sheer volume of hydrogen found in the plumes meant there was a "plentiful supply of food" for microbes to exist.
"We found that there was plenty of chemical energy in the interior ocean [of Enceladus] to drive microbial metabolism," he said.
Is there life on Enceladus?
But while Dr Waite said the findings were exciting, the researchers were "very agnostic" about the prospect of life in Enceladus' oceans.
"We have so much hydrogen relative to methane that one could argue there's no microbes around to eat it," he said.
"It begs the question, let's go back and find out if there's life there."
Dr Waite said the next order of business was either to return to the plumes of Enceladus with more precise instruments, or explore similar sub-surface oceans to the ones under the crust of the moon.
"Ultimately you want to send a submarine but it's going to be while before we can manage that one," he said.
Dr Waite said the Europa Clipper mission, which is set for a launch in the 2020s, provided an opportunity to extend the research.
"We've given some thought to this in putting together the Europa Clipper payload so that we'll go to Europa with some of the types of instruments [to conduct] investigations into presumably the plumes of Europa," he said.
The NASA New Frontiers program would also provide an opportunity to return to Enceladus with more sophisticated instruments, said Dr Waite.
The Cassini mission will come to a dramatic end when the spacecraft crashes into the surface of Saturn later this year.