To extend on the answer and comments of Derek Elkins.
Indeed, applying e.g. the covariant Yoneda lemma $\left[\,{\rm Nat}(\hom_{\mathcal C}(C,-),\,F)\,\simeq\,F(C)\right.$ for $\left. F:\mathcal C\to\mathcal Set\,\right]$ with $\mathcal C=\mathcal A^{op}\times\mathcal B$ and an arbitrary profunctor $F:\mathcal A^{op}\times\mathcal B\to\mathcal Set$ will produce
$$ {\rm Nat}(\hom_{\mathcal A^{op}\times\mathcal B}((A,B),\,-),\,F)\,\simeq\,F(A,B) $$
where $\hom_{\mathcal A^{op}\times\mathcal B}((A,B),\, (X,Y))=\hom_{\mathcal A}(X,A)\times\hom_{\mathcal B}(B,Y)$.
Let $H_{A,B}$ denote this profunctor $H_{A,B}(X,Y)=\hom_{\mathcal A}(X,A)\times\hom_{\mathcal B}(B,Y)$.
Observe that this is basically the same as considering the disjoint union $\mathcal A+\mathcal B$ and freely joining an arrow $h_{A,B}:A\to B$:
the set of arrows $X\to Y$ arising this way, for $X\in Ob\,\mathcal A,\ Y\in Ob\,\mathcal B$, consists exactly of formal compositions $\beta\circ h_{A,B}\circ\alpha$ for arbitrary $\alpha:X\to A$ and $\beta:B\to Y$.
(In the above setting, we have $h_{A,B}=(1_A,1_B)\in H_{A,B}(A,B)$.)
We can also view any profunctor $F:\mathcal A^{op}\times\mathcal B\to\mathcal Set$ as a category containing $\mathcal A+\mathcal B$ by considering $F(A,B)$ as the set of (hetero-)morphisms 'from $A$ to $B$'. Compositions are given by the action of $F$ on morphisms.
Also, natural transformations $F\to G$ simply correspond to functors that are identical on $\mathcal A+\mathcal B$.
From this perspective, it's clear that ${\rm Nat}(H_{A,B},\,F)\cong F(A,B)$, since any morphism of profunctors $\Phi:H_{A,B}\to F$ is indeed uniquely determined by its image on the freely joined arrow $h_{A,B}$ which can be any arrow $A\to B$ in $F$, i.e. any element of $F(A,B)$.
It's easy to see that both the covariant and the contravariant Yoneda lemmas are consequences of this instance, by letting either $\mathcal A$ or $\mathcal B$ be the trivial, one element category.
To answer your original question, the bivariate hom functor has less to do with Yoneda, nevertheless we can have a similar statement:
For any 'endoprofunctor' $F:\mathcal A^{op}\times\mathcal A\to\mathcal Set$, we have
$${\rm Nat}(\hom_{\mathcal A}(-,-),\,F)\,\simeq\,{\rm Nat}(I_1,I_2)\,\simeq\,\int_{\mathcal A}F$$
where $I_1,I_2:\mathcal A\to\mathcal F$ are the two embeddings of $\mathcal A$ into the category $\mathcal F$ constructed as above from $F$, and the integral denotes the end of $F$.
For the correspondence, observe that any natural transformation $\Phi:\hom_{\mathcal A}(-,-)\to F$ is determined by the images $t_A:=\Phi_{A,A}(1_A)\in F(A,A)$ of $1_A\in\hom_{\mathcal A}(A,A)$, and these elements $t_A$ need to satisfy a commutativity condition for each arrow $\alpha:A\to A'$.