"$1.98", a short story by Arthur Porges, first published in The Magazine of Fantasy and Science Fiction, May 1954, available at the Internet Archive.
As a high school student just starting in science fiction, I read a short story collection in paperback that included this story -- not quite a short-short, but not very long either. I think that it was written by a familiar author, since the collection was one of those 'Best Of .." anthologies.
Three and a half pages in its original magazine publication. Arthur Porges has a Wikipedia page; probably his most famous stories are "The Ruum" and "The Devil and Simon Flagg".
Our Hero is a sympathetic young guy trying to get ahead, in love with a beautiful neighbor, but hopeless in love.
That morning Will Howard was taking a Sunday stroll through the woods, a pleasure which lately had been shared and intensified by Rita Henry. Not even the bright sun, the bracing air, the unique song of a canyon wren, could lighten Will's dark thoughts. Right now she was out riding with Harley Thompson at an exclusive country club. Will couldn't blame her. Harley was six feet two, a former Princeton tackle; ruggedly handsome, full of pleasant small talk; the young-executive-with-a-big-future. And he, Will Howard, a skinny, tongue tied fellow—
He rescues a miniature Minor Deity (and I've forgotten the mechanism - rescued from a cat perhaps?)
It was a weasel:
Quickly Will scooped the terrified rodent into one palm. The weasel stopped, making a nasty, chikkering sound, eyes red in the triangular mask of ferocity that was its face. For a heartbeat it seemed about to attack its giant opponent, but as Will stepped forward, shouting, the beast, chattering with rage, undulated off the path.
and gets a wish in return.
In a voice which although faint was surprisingly resonant, the figure said: "Accept, O kindly mortal, the grateful thanks of Eep, the God. How can I reward you for saving me from that rapacious monster?"
The catch is that since this is only a minor deity, the value of the wish is small - and I forget the actual value, perhaps $2.49.
"You mentioned a—a reward," he said diffidently.
"I certainly did," the god assured him, swinging on a dandelion stem and kicking minute bare feet luxuriously. "But alas, only a small one. I am, as you see, a very small god."
"Oh," Will said, rather crestfallen. Then brightening: "May I suggest that a small fortune—?" Truly the presence of an immortal was sharpening his wits.
"Of course. But it would have to be exceedingly small. I couldn't go above $1.98."
Later that evening, the girl knocks on the door, he opens it to her welcoming arms, and the night passes. The next morning, Our Hero finds a small clipping on the floor, an article stating the latest estimates of the total value of the elements in the human body were... $2.49. (The whole story was building to that punch line.)
The next morning, when she picked up the wispy panties from the floor where they had been tossed in flattering haste, a scrap of paper dropped from the black nylon.
Wondering, Will picked it up. It was a newspaper clipping. Someone had written in the margin in a tiny, flowing script: "A gratuity from the grateful (up to $1.98) God Eep."
The clipping itself, a mere filler, read: "At present prices, the value of the chemical compounds which make up the human body is only $1.98."