We study the vertex-decremental Single-Source Shortest Paths (SSSP) problem: given an undirected graph $G=(V,E)$ with lengths $ell(e)geq 1$ on its edges and a source vertex $s$, we need to support (approximate) shortest-path queries in $G$, as $G$ undergoes vertex deletions. In a shortest-path query, given a vertex $v$, we need to return a path connecting $s$ to $v$, whose length is at most $(1+epsilon)$ times the length of the shortest such path, where $epsilon$ is a given accuracy parameter. The problem has many applications, for example to flow and cut problems in vertex-capacitated graphs. Our main result is a randomized algorithm for vertex-decremental SSSP with total expected update time $O(n^{2+o(1)}log L)$, that responds to each shortest-path query in $O(nlog L)$ time in expectation, returning a $(1+epsilon)$-approximate shortest path. The algorithm works against an adaptive adversary. The main technical ingredient of our algorithm is an $tilde O(|E(G)|+ n^{1+o(1)})$-time algorithm to compute a emph{core decomposition} of a given dense graph $G$, which allows us to compute short paths between pairs of query vertices in $G$ efficiently. We believe that this core decomposition algorithm may be of independent interest. We use our result for vertex-decremental SSSP to obtain $(1+epsilon)$-approximation algorithms for maximum $s$-$t$ flow and minimum $s$-$t$ cut in vertex-capacitated graphs, in expected time $n^{2+o(1)}$, and an $O(log^4n)$-approximation algorithm for the vertex version of the sparsest cut problem with expected running time $n^{2+o(1)}$. These results improve upon the previous best known results for these problems in the regime where $m= omega(n^{1.5 + o(1)})$.