In this article, we present a combinatorial formula for the Wedderburn decomposition of rational group algebras of nested GVZ $p$-groups, where $p$ is an odd prime. Using this formula, we derive an explicit combinatorial expression for the Wedderburn decomposition of rational group algebras of all two-generator $p$-groups of class $2$. Additionally, we provide explicit combinatorial formulas for the Wedderburn decomposition of rational group algebras of certain families of nested GVZ $p$-groups with arbitrarily large nilpotency class. We also classify all nested GVZ $p$-groups of order at most $p^5$ and compute the Wedderburn decomposition of their rational group algebras. Finally, we determine a complete set of primitive central idempotents for the rational group algebras of nested GVZ $p$-groups.