The weighted Szeged index and the weighted vertex-PI index of a connected graph $G$ are defined as $wSz(G) = \sum_{e=uv \in E(G)} (deg (u) + deg (v))n_u(e)n_v(e)$ and $wPI_v(G) = \sum_{e=uv \in E(G)} (deg(u) + deg(v))( n_u(e) + n_v(e))$, respectively, where $n_u(e)$ denotes the number of vertices closer to $u$ than to $v$ and $n_v(e)$ denotes the number of vertices closer to $v$ than to $u$. Moreover, the weighted edge-Szeged index and the weighted PI index are defined analogously. As the main result of this paper, we prove that if $G$ is a connected graph, then all these indices can be computed in terms of the corresponding indices of weighted quotient graphs with respect to a partition of the edge set that is coarser than the $Θ^*$-partition. If $G$ is a benzenoid system or a phenylene, then it is possible to choose a partition of the edge set in such a way that the quotient graphs are trees. As a consequence, it is shown that for a benzenoid system the mentioned indices can be computed in sub-linear time with respect to the number of vertices. Moreover, closed formulas for linear phenylenes are also deduced. However, our main theorem is proved in a more general form and therefore, we present how it can be used to compute some other topological indices.