During an alien invasion of earth, the protagonist and his minister friend find God (yes, THE God) in the invaders' camp. Short story or novella in anthology. Published in early 1960s, read in the early 1960s.
"For I Am a Jealous People", a 1954 novella by Lester del Rey. It has appeared under various covers. In the early 1960s you might have read it in the 1963 printing of Star Short Novels edited by Frederik Pohl.
The story begins with the assumption that Yahweh—the original one-goat God of the Hebrews, spiteful, petulant and arbitrary—really exists, and that He has found Himself a new chosen people and turned against us. This is novel enough, and del Rey's solution is neat, shocking and sensible. The two together occupy, legitimately, about fifteen pages. The rest is vehicle, almost thirty dismal pages of it, including a pointless escape-and-capture sequence that might have been lifted bodily from any two-bit action novel.
Excerpt from the story:
There were two elaborately robed priests kneeling in the center of the chapel. But his eye barely noticed them before it was attracted to what stood in front of the new altar.
A box of wood stood on an earthenware platform. On it were four marks, which his eyes recognized as unfamiliar, but which his mind twisted into a sequence from the alphabets he had learned, unpronounceable yet compelling. And above the box was a veil, behind which Something shone brightly without light.
In his mind, a surge of power pulsed, making patterns that might almost have been words through his thoughts—words like the words Moses once heard—words that Amos, heartsick, knew. . . .
"I AM THAT I AM, who brought those out of bondage from Egypt and who wrote upon the wall before Belshazzar, MENE, MENE, TEKEL, UPHARSIN, as it shall be writ large upon the Earth, from this day forth. For I have said unto the seed of Mikhtchah, thou are my chosen people and I shall exalt thee above all the races under the heavens!"
[. . . .]
The seed of Mikhtchah. The seed of the invaders. . . .
The old man sighed, running his hands along the rifle. "I ain't leaving my store for any bunch of aliens. And if the Lord I been doing my duty by all my life decides to put Himself on the wrong side, well, maybe He'll win. But it'll be over my dead body!"
"I have come back from captivity among the aliens," he began. "I have seen the hordes who have no desire but to erase the memory of man from the dust of the earth that bore him. I have stood at the altar of their God. I have heard the voice of God proclaim that He is also our God, and that He has cast us out. I have believed Him, as I believe Him now."
[. . . .]
"God has ended the ancient covenants and declared Himself the enemy of all mankind," Amos said, and the chapel seemed to roll with his voice. "I say this to you: He has found a worthy opponent."