The answer is "yes". More precisely, $f$ arises from the $q$-Frobenius of the *split* descent down to the prime field $\mathbf{F}_ p$.  To see this, let $(G_0, T_0)$ be such a descent, and $F_0:(G_0, T_0) \rightarrow (G_0,T_0)$ the $q$-Frobenius morphism.  This induces the self-map of the root datum given by $q$-multiplication on ${\rm{X}}(T_0)$.  Extending scalars to $k$ has no effect on the root datum for split groups, so $(F_ 0)_ k$ induces the endomorphism of the root datum of $((G_ 0)_ k, (T_ 0)_ k)$ given by $q$-multiplication on the root datum.  Pick a $k$-isomorphism between the $k$-split pairs $(G,T)$ and $((G_ 0)_ k, (T_ 0)_ k)$.  The resulting isomorphism of root data identifies the maps from $(F_ 0)_ k$ and $f$ since $q$-multiplication is functorial with respect to all homomorphisms between abelian groups. Thus, these maps coincide up to the action of some $t \in \overline{T}(k) = (\overline{T}_ 0)(k)$, where 
$\overline{T} := T/Z_G$ and 
$\overline{T}_ 0 := T_ 0/Z_ {G_ 0}$ are the "adjoint tori''.  Using an isomorphism 
$\overline{T}_ 0 \simeq \mathbf{G}_m^r$, $t$ goes over to some $r$-tuple $(t_i)$ with $t_i \in k^{\times}$.  Since $k$ is separably closed, we can solve $t_i = y_i^{q-1}$ with $y_i \in k^{\times}$.  In other words, $t = f(y)/y$ for some $y \in T_0(k)$.  So if we modify the identification of $(G_0, T_0)$ as an $\mathbf{F}_ p$-descent of $(G,T)$ by composing with the action of $y$ or $y^{-1}$ (depending on direction of maps) then $f = (F_ 0)_ k$ via the new identification of $(G_ 0, T_ 0)$ as a split $\mathbf{F} _p$-descent of $(G,T)$.
QED

Note that the above works over any separably closed field of characteristic $p > 0$, not necessarily algebraically closed, provides the Isomorphism Theorem is valid over such fields.  The Existence, Isomorphism, and even Isogeny Theorems are valid for split connected reductive groups over any field.  The paper of Steinberg mentioned by Kevin is really nice, but unfortunately assumes from the outset that the ground field is algebraically closed.  Good news, in case you may care, is that one can deduce the results over any field from that case as a "black box'' by using descent theory.  See Appendix A.4 of the book "Pseudo-reductive groups''.