This paper provides a finite difference discretization for the backward Feynman-Kac equation, governing the distribution of functionals of the path for a particle undergoing both reaction and diffusion [Hou and Deng, J. Phys. A: Math. Theor., {\bf51}, 155001 (2018)]. Numerically solving the equation with the time tempered fractional substantial derivative and tempered fractional Laplacian consists in discretizing these two non-local operators. Here, using convolution quadrature, we provide a first-order and second-order schemes for discretizing the time tempered fractional substantial derivative, which doesn't require the assumption of the regularity of the solution in time; we use the finite difference method to approximate the two-dimensional tempered fractional Laplacian, and the accuracy of the scheme depends on the regularity of the solution on $\bar{\Omega}$ rather than the whole space. Lastly, we verify the predicted convergence orders and the effectiveness of the presented schemes by numerical examples.