Here is the text from the book Topology by Munkres:
Studying equivalence relations on a set $A$ and studying partitions of $A$ are really the same thing. Given any partition $\scr D$ of $A$, there is exactly one equivalence relation on $A$ from which it is derived.
The proof is not difficult. To show that the partition $\scr D$ comes from some equivalence relation, let us define a relation $C$ on $A$ by setting $xCy$ if $x$ and $y$ belong to the same element of $\scr D$. Symmetry of $C$ is obvious; reflexivity follows from the fact that the union of the elements of $\scr D$ equals all of $A$; transitivity follows from the fact that distinct elements of $\scr D$ are disjoint. It is simple to check that the collection of equivalence classes determined by $C$ is precisely the collection $\mathscr{D}$.
To show there is only one such equivalence relation, suppose that $C_1$ and $C_2$ are two equivalence relations on $A$ that give rise to the same collection of equivalence classes $\mathscr{D}$. Given $x\in A$, we show that $yC_1 x$ if and only if $yC_2 x$, from which we conclude that $C_1=C_2$. Let $E_1$ be the equivalence class determined by $x$ relative to the relation $C_1$; let $E_2$ be the equivalence class determined by $x$ relative to the relation $C_2$. Then $E_1$ is an element of $\scr D$, so that it must equal the unique element of $D$ of $\scr D$ that contains $x$. Similarly, $E_2$ must equal $D$. Now by definition, $E_1$ consists of all $y$ such that $yC_1x$; and $E_2$ consists of all $y$ such that $yC_2x$. Since $E_1=D=E_2$, our result is proved.
The text of course proves that $yC_1x \iff yC_2x$, but why it implies $C_1 = C_2$? For example suppose elements are humans, so we can define $C_1$ for "person x and person y are in relation $C_1$ if each of them has two hands"; and, $C_2$ for "person x and person y are in relation $C_2$ if each of them has two foots". $yC_1x \iff yC_2x$ holds but $C_1 \ne C_2$?
Edit - PS - we ignore the set of people with two foots and less than two hand and with two hands and less than two foots.
There are persons with two foots and less than two hands; so there is no $\iff$ relationship between the two
The source of the confusion here is what $C_1=C_2$ means; since there is no "intrinsic way" to know what does it mean for two completely abstract relationships to be equal, we call them equal if they act in the same way.