I'm trying to prove the next theorem:
Let $\mathfrak{g}$ be a complex semisimple Lie algebra of type $A_3$, $\mathfrak{h}$ a Cartan subalgebra, $R$ a root system associated to the pair $(\mathfrak{g},\mathfrak{h})$ and $\Delta=\{\alpha_1,\alpha_2,\alpha_3\}$ a basis of simple roots. Let $(x_i,h_i,y_i)$ be the $\mathfrak{sl}_2$-triple associated to each simple root $\alpha_i$, $i=1,2,3$, and $\sigma$ be the automorphism of $\mathfrak{g}$ induced by the automorphism of $R$ which interchanges $\alpha_1$ and $\alpha_3$ and fixes $\alpha_2$. Then $x_1+x_3$, $x_2$, $y_1+y_3$ and $y_2$ generate the subalgebra $\mathfrak{g}^\sigma$ of fixed points, and it is a semisimple Lie algebra of Type $B_2$.
I know that by the semisimplicity of $\mathfrak{g}$, we have a deocmposition $\mathfrak{g}=\mathfrak{h}\oplus\bigoplus\limits_{\alpha\in R^*}\mathfrak{g}_{[\alpha]}$ and $x_i\in\mathfrak{g}_{[\alpha_i]}$, $y_i\in\mathfrak{g}_{[-\alpha_i]}$ for every $i=1,2,3$, so if $\sigma$ interchanges $\alpha_1$ and $\alpha_3$ and fixes $\alpha_2$, then it interchanges $x_1$ with $x_3$, $y_1$ with $y_3$ and fixes $x_2$ and $y_2$, so $x_1+x_3$, $x_2$, $y_1+y_3$ and $y_2$ are all in $\mathfrak{g}^\sigma$. But I don't know how to conclude that they generate that subalgebra, or that it is of type $B_2$. I would appreciate any hints or comments about this.
"The automorphism of $\mathfrak{g}$ induced by the automorphism of $R$" is actually a bit ambiguous, but it's clear from context that they mean the automorphism that switches $x_1 \leftrightarrow x_3$, $y_1 \leftrightarrow y_3$ and fixes $x_2$ and $y_2$. It's probably a good exercise to check that this indeed defines an automorphism and determines it completely.
In fact, let's switch to Chevalley basis notation and call
where according to what they call an $\mathfrak{sl}_2$-triple in your source you might have to throw in some minus signs in the second line.
In any case, it's a good exercise to recall that these twelve $e$'s (each of them being a basis of the root space to the root in its index), together with $h_1, h_2$ and $h_3$, are a vector space basis of $\mathfrak{g}$, and the one we want to work with: Because it makes the automorphism completey explicit. E.g, it also switches $h_1 \leftrightarrow h_3$, $e_{\alpha_1+\alpha_2} = [x_1,x_2] \leftrightarrow -[x_2,x_3] = - e_{\alpha_2+\alpha_3}$, and fixes $h_2$ as well as $e_{\alpha_1+\alpha_2+\alpha_3}$.
It's linear algebra to see that a vector space basis of the fixed space $\mathfrak{g}^\sigma$ is:
Setting $e_{\beta_1} := e_{\alpha_1}+e_{\alpha_3}$ and $e_{\beta_2} := e_{\alpha_2}$, compute how nicely
$[e_{\beta_1}, e_{\beta_2}] = e_{\alpha_1+\alpha_2}-e_{\alpha_2+\alpha_3} =: e_{\beta_1+\beta_2}$
and $[e_{\beta_1}, e_{\beta_1 +\beta_2}] = -2e_{\alpha_1+\alpha_2+\alpha_3} =: e_{2\beta_1 + \beta_2}$ etc.
so that $\beta_1$ and $\beta_2$ are a a basis of a root system of type $B_2$, with $\beta_1$ being the short root. Check further that $\mathfrak{h}^\sigma$ indeed acts on those new root spaces, with $h_1+h_3$ of course being the coroot of $\beta_1$, and $h_2$ the coroot of $\beta_2$. So $\mathfrak{g}^\sigma$ decomposes as $\mathfrak{h}^\sigma \oplus $ root spaces, and hence is semisimple of type $B_2$.
It is another exercise to see how this, written out in matrices, modulo some choices (scalings and signs I would guess), is the same as what happens in Andreas Cap's answer, just from a very different viewpoint.