A relation $R$ over a set $X$ needs to satisfy three properties in order to be an equivalence relation:
It must be reflexive, that is, every element in $X$ is related to itself. $\forall x\in X: xRx$;
It must be symmetric, that is, if $x$ is related to $y$, $y$ must be related to $x$. $xRy \implies yRx$;
It must be transitive, that is, if $x$ is related to $y$ and $y$ is related to $z$, $x$ must be related to $z$.
Let me stress that you have defined $\sim$ as:
$(x,y,z) \sim (a,b,c) \iff (x,y,z) = -(a,b,c)$
Unfortunately, that violates the reflexive property, that is, we don't have that $(x,y,z)$ is equivalent to itself for all triples $(x,y,z) \in S^2$. Take $(1,0,0)$ for example. If $\sim$ is reflexive, then we must have $(1,0,0) \sim (1,0,0) \iff (1,0,0) = -(1,0,0)$ by definition. But $1 \neq -1$ so it is not reflexive.
I believe this problem arises because of the way the problem was worded to you. In English, one could say, for example, "show that the relation we get by identifying all points $(x,y,z)$ with $-(x,y,z)$ is an equivalence relation." Although it looks the same, it is not the same as you wrote.
Or you could see written, "prove that $\sim$ is an equivalence relation if $(x,y,z) \sim -(x,y,z)$"; which would read as I wrote just above, being implicit that every element $(x,y,z)$ is related to itself, in addition to being related to $-(x,y,z)$.
If this was what was meant when the problem was handed to you, then yes we have an equivalence relation.
If that is the case, if we are to take implicitly that $(x,y,z)$ is related to itself, then the reflexive property is true by definition of the relation.
The symmetric property is shown by:
$$(x,y,z) \sim (a,b,c) \iff \begin{cases}(a,b,c) = -(x,y,z)\iff -(a,b,c) = (x,y,z)\ \text{or}\\(a,b,c) = (x,y,z)\end{cases}\tag{1}$$
And we would have symmetry if it is true that $(a,b,c) \sim (x,y,z)$. But
$$(a,b,c) \sim (x,y,z) \iff \begin{cases}(x,y,z) = (a,b,c)\ \text{or}\\(x,y,z) = -(a,b,c)\end{cases}\tag{2}$$
But either case we need in $(2)$ happens in $(1)$ and every case that can happen in $(1)$ is needed in $(2)$, thus we have symmetry.
Can you do something similar to show the transitivity?