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I was wondering about this after I realised that Dr. Isaacs in Resident Evil wants to wipe out humanity again and then restart it with a chosen few so life stands a better chance.

Dr. Isaacs: I propose that we end the world... But on our terms. An orchestrated apocalypse. One that would cleanse the world of its' population but leave its infrastracture and resources intact. It's been done once before. With great success. The chosen few will ride out the storm, not in an ark as in the book of Genesis, but in safety. Underground. And when it's over, We will emerge onto a cleansed Earth. One we can then reboot. In our image.

_{Resident Evil: The Final Chapter}

And that Thanos from Marvel has a similar idea but on a universal scale. I know that his motivations aren't the same in the original The Infinity Gauntlet comics but in the MCU and specifically Avengers: Infinity War he wants to do it so life can succeed.

Thanos: Little one, it's a simple calculus. This universe is finite, its resources finite. If life is left unchecked, life will cease to exist. It needs correction.

_{Avengers: Infinity War}

But, what was the first work which brought about the idea of deliberately wiping out half of humanity, a species, life, a planet, a universe in order for it to survive?

1950: "The New Reality", a novelette by Charles L. Harness, first published in Thrilling Wonder Stories, December 1950, available at the Internet Archive.

Professor Luce, a mad ontologist, constructs a device with which he intents to reset reality, expecting that only a select few (himself included of course) will survive.

Prentiss drew deeply on his pipe.

"I saw it."

"Did you understand it?"

"No. It wasn't all there. At least, the apparatus on the table was incomplete. There's more to it than a Nicol prism and a goniometer."

"Ah, you are clever! Yes, I was wise in not permitting you to remain very long — no longer than necessary to whet your curiosity. Look, then! I offer you a partnership. Check my data and apparatus; in return you may be present when I run the experiment. We will attain enlightenment together. We will know all things. We will be gods!"

"And what about two billion other human beings?" said Prentiss, pressing softly at his shoulder holster.

The professor smiled faintly. "Their lunacy — assuming they continue to exist at all — may become slightly more pronounced, of course. But why worry about them?" The wolf-lip curled further. "Don’t expect me to believe this aura of altruism, Mr. Prentiss-Rogers. I think you're afraid to face what lies behind our so-called 'reality.'"

[. . . .]

He knew in a brief flash of insight, that for sentient, thinking beings, Time
had suddenly become a barricade rather than an endless road.

The exploding bomb — the caving cottage walls — were hanging, somewhere, frozen fast in an immutable, eternal stasis.

Luce had separated this fleeting unseen dimension from the creatures and things that had flowed along it. There is no existence without change along a temporal continuum. And now the continuum had been shattered.

Was this, then the fate of all tangible things — of all humanity?

Were none of them — not even the two or three who understod advanced ontology, to — get through?

[. . . .]

She'd got through!

The whole world, and just the two of them!

His heart was pounding ecstatically as he began to run lithely upwind.

And they’d keep it this way, simple and sweet, forever, and their children
after them. To hell with science and progress! (Well, within practical limits, of course.)

As he ran, there rippled about his quivering nostrils the seductive scent of
apple blossoms.

Probably not the first, but:

1964. In Stanley Kubrick's movie Dr. Strangelove, towards the end, with impending nuclear war in sight, the titular character suggests gathering a few hundred thousand selected people (including, of course, top politicians and military personnel) underground to wait for the surface to become habitable again, repopulating the planet. He suggests a 10:1 female/male ratio for faster breeding - which isn't rational in my opinion, since it would probably take several generations before the surface becomes habitable again and you don't want the underground habitat to become overpopulated. But of course, the outlook of having access to plenty of women helps persuade the decision-makers to adopt the plan.

The basic concept long pre-dates the science-fiction and fantasy genres: it's a widespread theme in mythology and religion. In addition to the well-known Biblical story of Noah, the Mesopotamians, Mayans, Chinese, Australian Aboriginies, and many others all had flood myths. For non-flood destruction, the Greek Silver Age ended with Zeus destroying the human race for impiety, and in some versions of the story, Talos, the bronze guard of Crete, is a remnant of another destruction. Among the natives of the southwestern United States, the Hopi Four Worlds creation narrative tells of three consecutive destructions of the human race for misbehavior, and surrounding areas have variations on this story, often with five worlds. There are probably also other examples I can't remember right now.

With this sort of existing tradition to draw on, asking "which SFF work first had the idea?" isn't really a meaningful question. It's more a matter of where you draw the line between fantasy and mythology.

I think that Jack Chalker's Well World series is the best answer. But it's not really the antagonist who does the reset, it's the protagonist, Nathan Brazil.

The Well World Page (Geocities)

The Stories

Of the Well World stories, the first (single volume) and the fourth (multi-volume) end with the arrival of all Entries at the Well
of Souls. They are judged by Nathan Brazil, who sends the baddies to
some awful punishment and the good guys to a second chance at doing
right (or back to simply live out the lives they were already living);
Brazil then goes back to being who he was in normal human space.

The second story (multi-volume, comprising the second and third volumes) does not have Brazil, although he is later revealed to have
influenced some of the events in that tale; Obie assumes the deus ex
machina role, although only Mavra Chang is aware of Obie's full role
in the events.

The third story (multi-volume) ends with Nathan Brazil and Mavra Chang resetting the Well of Souls, deleting and then recreating the
universe, repopulating it, etc., before they also return to Earth.

The fifth tale does not have Brazil at all; although he is mentioned, it is not by name, although they do mention that he is of
the human species. Some of the Entries that survive return to the
Realm as human beings.

Also, see Well World Series (wikipedia)