They are saying the same thing, at a fundamental level - it's just that the implementation is a bit different. The first equation you noted is valid throughout the system because it solves for the intrinsic values throughout the system, such as the local current density and local electric potential.
The second equation you mentioned is a lumped-value equation, that is technically valid throughout the system, but by the way you wrote it, I'm guessing that $\mathbf{V}$, $\mathbf{R}$, and $\mathbf{I}$ have units of voltage ($V$), resistance ($\Omega$), and current ($I$), respectively. The question is then, voltage where? Current where? Resistance where?
When modeling a continuum physics problem it's beneficial to reduce everything into its intrinsic properties instead of extrinsic properties, which means that you end up working with scale-independent quantities.
Now back to your first equation:
$$ \mathbf{J} = \sigma \mathbf{E} $$ is the same as $$ \mathbf{E} = \frac{1}{\sigma} \mathbf{J} $$
It's good to remember that conductivity ($\sigma$, with units Siemens/meter) is just the reciprocal of resistivity ($\rho$), which has units of $\Omega \cdot m$. Thus
$$ \mathbf{E} = \rho \mathbf{J} $$
This is more or less the valid local equation that an FEM solver would solve at each node in the problem domain, and which most resembles your global equation of Ohm's law.
For a more comprehensive answer to how resistivity relates to conductivity, resistance, and conductance, check out the wiki article on exactly this topic:
https://en.wikipedia.org/wiki/Electrical_resistivity_and_conductivity