Joule dissipation (equivalently, Ohmic heating) is a statistical process. It doesn't occur at the microscopic scale, and a single travelling electron in an electrical field is certainly microscopic. Resistivity depends on particle collisions, which turns translational kinetic energy into thermal kinetic energy.
Ohm's law relates the current $\vec{j}$ in a medium to the electric field $\vec{e}$ via the conductivity $\sigma$,
$$ \vec{j}=\sigma \vec{e} $$
Another way of looking at this is that dissipation $P$ is given by
$$P=\frac{j^2}{\sigma}$$
Written this way, we have an expression very similar to that for Ohmic heating in a resistor, namely that
$$P=I^2 R$$
Since the conductivity is the inverse of the resistivity, this is an intuitive result.
The advantage of Joule's expression is that it allows for the determination of Joule heating at a particular point in space, rather than over the entire resistor (whatever that may be). This is useful in plasma physics, for example, where it may be the case that Joule heating is localized, rather than uniform throughout the plasma. Nonetheless, it is predicated on the medium being strongly collisional, and still must refer to a macroscopic, rather than microscopic effect.