"The New Reality", a novelette by Charles L. Harness, also my (unaccepted) answer to this old question and this one; first published in Thrilling Wonder Stories, December 1950, available at the Internet Archive. The story matches your description, but Bishop Berkeley is not mentioned. Does any of these covers look familiar?
The ontologist continued rapidly. "All of you doubt my sanity. A week ago I would have, too. But since then I've done a great deal of research in the history of science. and I repeat, the universe is the work of man. I believe that man began his existence in some incredibly simple world—the original and true noumenon of our present universe. And that over the centuries man expanded his little world into its present vastness and incomprehensible intricacy solely by dint of imagination.
"Consequently, I believe that what most of you call the 'real' world has been changing ever since our ancestors began to think."
The mad scientist's experiment:
"Your apparatus," said Prentiss, "is going to provide just such a photon. And I think it will be a highly confused little photon, just as your experimental rat was, that night not so long ago. I think it was Schroedinger who said that these physical particles were startlingly human in many of their aspects. Yes, your photon will be given a choice of equal probability. Shall he reflect? Shall he refract? The chances are 50 percent for either choice. He will have no reason for selecting one in preference to the other.
There will have been no swarm of preceding photons to set up a traffic guide
for him. He'll be puzzled; and trying to meet a situation for which he has no
proper response, he'll slow down. And when he does, he'll cease to be a photon, which must travel at the speed of light or cease to exist. Like your rat, like many human beings, he solves the unsolvable by disintegrating."
Luce said : "And when it disintegrates, there disappears one of the lambdas that hold together the Einstein space-time continuum. And when that
goes, what's left can be only final reality untainted by theory or imagination. Do you see any flaw in my plan?"
The end of the world:
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 understood advanced ontology—to get through?
There was nothing but a black, eerie silence all around.
And what about Luce?
Had the demonic professor possessed sufficient mental elasticity to slip through?
He'd soon know.
The ontologist relaxed again, and began floating through a dreamy patch of light and darkness. A pale glow began gradually to form about his eyes, and shadowy things began to form, dissolve, and reform.
He felt a great rush of gratitude. At least the shape of final reality was to be visible.
And then, at about the spot where Luce had stood, he saw the Eyes—two tiny red flames, transfixing him with unimaginable fury.
An unholy aura was playing about the sinuous shadow that contained the jeweled flames. Those eyes were brilliant, horrid facets of hate in the head of a huge, coiling serpent-thing! Snake-Eyes!
The new Adam and Eve:
Meta-universe, by whatever name you called it, was beautiful, like a gorgeous garden. What a pity he must live and die here alone, with nothing but a lot of animals for company. He’d willingly give an arm, or at least a rib, if — "Adam Prentiss! Adam!"
He whirled and stared toward the orchard in elated disbelief.
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.