Qubits, which are the quantum counterparts of classical bits, are used as basic information units for quantum information processing, whereas underlying physical information carriers, e.g., (artificial) atoms or ions, admit encoding of more complex multilevel states—qudits. Recently, significant attention has been paid to the idea of using qudit encoding as a way for further scaling quantum processors. In this work, we present an efficient decomposition of the generalized Toffoli gate on five-level quantum systems—so-called ququints—that use ququints’ space as the space of two qubits with a joint ancillary state. The basic two-qubit operation we use is a version of the controlled-phase gate. The proposed N-qubit Toffoli gate decomposition has O(N) asymptotic depth and does not use ancillary qubits. We then apply our results for Grover’s algorithm, where we indicate on the sizable advantage of using the qudit-based approach with the proposed decomposition in comparison to the standard qubit case. We expect that our results are applicable for quantum processors based on various physical platforms, such as trapped ions, neutral atoms, protonic systems, superconducting circuits, and others.