Per Gazerun's comment answer to related question which leads to relaxation of the OP.
This is possible over the integers for all $d$ and the question can be relaxed by allowing finitely many points over the rationals.
First we define the set $\{1,-1\}$ with the equation $(m-1)(m+1)=0$.
The only integers solutions to $x^2-m n^2y^2=1$ are $x=\pm 1, ny=0$ and $y=\pm 1,x=0$ and $n=\pm 1,x=0$.
Over $\mathbb{Z}[\sqrt{d}]$ for $n=\sqrt{d}$ this is Pell equation $x^2 \pm ny^2=1$ with infinitely many solutions and if $d$ is square we are in the above case.
So we must get rid of the bad points $x=\pm 1,0$.
Use the following cheap trick: $ (x^2-1)x z = 1$. This is linear in $z$ unless $(x^2-1)x=0$ which leads to $0=1$.
So our final system of equations is $(m-1)(m+1)=0,x^2-m n^2y^2=1, (x^2-1)x z = 1$ which doesn't have integer solutions but have infinitely many over $\mathbb{Z}[\sqrt{d}]$ for all $d$. If $d$ is negative chose $m=-1$ otherwise $m=1$
Partial result, some one could try to extend it.
It is possible to define variety the complement of $x=y^2$, that is $x \ne y^2$:
$$ zt=1 \qquad (1)$$ $$ (x-y^2) z=1 \qquad (2)$$.
In (1) and (2) $z$ can be any nonzero rational. $x\ne y^2$ for obvious reasons and $x-y^2=1/z$.
Appears to me this allows to describe the complement of variety given by single equation.