The small leather-bound books are worth many millions of pounds and include the scientist's "tree of life" sketch.
Their return comes 15 months after the BBC first highlighted they had gone missing and the library launched a worldwide appeal to find them.
"I feel joyous," the university's librarian Dr Jessica Gardner says.
She grins broadly as she breaks the news. In fact, she cannot stop smiling. "They're safe, they're in good condition, they're home."
But who returned the two postcard-sized notepads is a real whodunit. They were left anonymously in a bright pink gift bag containing the original blue box the notebooks were kept in and a plain brown envelope.
On it was printed a short message: "Librarian, Happy Easter X."
Inside were the two notebooks, wrapped tightly in cling film. The package had been left on the floor, in a public part of the library with no CCTV, outside Dr Gardner's office.
"I was shaking," says Dr Gardner of her reaction to seeing the bag and its contents for the first time on 9 March. "But I was also cautious because until we could unwrap them, you can't be 100% sure."
An agonising delay of five days followed between finding the package and the police granting permission to open the cling film, examine the notebooks and confirm they were genuine.
"There have been tears," says Dr Gardner sheepishly. "And I think there still will be, because we are not over the emotional rollercoaster. It means so much to us to have these home."
She admits she had feared the notebooks would not be returned in her lifetime. "I thought it might take years. My sense of relief at the notebooks' safe return is profound and almost impossible to adequately express.
"I was heartbroken to learn of their loss and my joy at their return is immense."
The notepads date from the late 1830s after Darwin had returned from the Galapagos Islands. On one page, he drew a spindly sketch of a tree, which helped inspire his theory of evolution and more than 20 years later would become a central theory in his groundbreaking work On the Origin of Species.
"The theory of natural selection and evolution is probably the single most important theory in the life and earth environmental sciences and these are the notebooks in which that theory was put together," says Jim Secord, emeritus professor of history and philosophy of science at Cambridge University.
"They're some of the most remarkable documents in the whole history of science."
The manuscripts were last seen in November 2000 after "an internal request" to remove them from the library's special collections strongroom to be photographed.
It was only during a routine check two months later that they were found to be missing. Initially, librarians thought they had been put back in the wrong place in the vast university library, which contains more than 10 million books, maps and manuscripts.
But despite various searches, the notebooks never turned up, and in 2020 Dr Gardner concluded they had probably been stolen. She called in the police and informed Interpol.
Prof Secord was one of several academics and experts who examined the returned manuscripts and concluded they were authentic. He took me through the "lines of evidence" they looked for.
"Darwin uses different types of ink in the notebooks. For example, on the famous tree of life page, there is both a brown ink and also a grey ink. Those kind of changes are quite difficult to forge convincingly.
"You can see the tiny bits of copper that are coming off where the hinges are located. The paper type is the right sort of paper.
"These are the tiny telltale signs that the whole team of researchers at the university library can use to tell that they're genuine."
The notebooks, adds Dr Gardner, are "in remarkably good condition". She confirms: "Every page that should be there is there."
She says: "I do wonder where they have been. They haven't been handled much, they've clearly been looked after with care, wherever they have been.
"I think what we can probably surmise is they've been dry, they haven't been subject to damp. So what can we speculate, other than that whoever had them, put them in a safe place?"
The notebooks are now being kept in a secure strongroom at the library, although they will go on public display in July as part of a free exhibition titled Darwin in Conversation.
But so many intriguing questions remain. Who took the notebooks? And who returned them?
Security cameras may eventually provide some clues. Although there was no CCTV in place on the landing where the gift bag was left last month, there are cameras outside the building monitoring the front and back of the library as well as the specialist reading rooms and the vaults inside.
"We have passed the CCTV that we have available to the police," says Dr Gardner. "That's a matter for their live investigation."
In the meantime, Cambridgeshire Police said: "Our investigation remains open and we are following up some lines of inquiry. We also renew our appeal for anyone with information about the case to contact us."