Quantum computing with qudits is an emerging approach that exploits a larger, more connected computational space, providing advantages for many applications, including quantum simulation and quantum error correction. Nonetheless, qudits are typically afflicted by more complex errors and suffer greater noise sensitivity which renders their scaling difficult. In this work, we introduce techniques to tailor arbitrary qudit Markovian noise to stochastic Weyl–Heisenberg channels and mitigate noise that commutes with our Clifford and universal two-qudit gate in generic qudit circuits. We experimentally demonstrate these methods on a superconducting transmon qutrit processor, and benchmark their effectiveness for multipartite qutrit entanglement and random circuit sampling, obtaining up to 3× improvement in our results. To the best of our knowledge, this constitutes the first-ever error mitigation experiment performed on qutrits. Our work shows that despite the intrinsic complexity of manipulating higher-dimensional quantum systems, noise tailoring and error mitigation can significantly extend the computational reach of today’s qudit processors.