The chromo-magnetic monopoles (CMM), emergent topological excitations of non-Abelian gauge fields carrying chromo-magnetic charge, have long been postulated to play an important role in the vacuum confinement of quantum chromodynamics (QCD), the deconfinement transition at temperature $T_c\approx 160\rm MeV$, as well as the strongly coupled nature of quark-gluon plasma (QGP). While such CMMs were found to help provide resolutions for challenging puzzles from heavy-ion collision measurements, they were typically introduced as model assumptions in the past. Here we perform a data-driven Bayesian inference of the chromo-magnetic component, within the CUJET framework, and extract its temperature-dependent abundance for the first time. Using the framework for calculations of jet energy loss and analyzing a comprehensive experimental data set for nuclear modification factor ($R_{AA}$) and elliptic flow ($v_2$) of high-transverse-momentum hadrons, the fraction of CMMs in the QGP is obtained by Bayesian inference and is found to be substantial in the $1\sim 2T_c$ region. The posterior CMM fraction is further tested against additional data and is also shown to predict QGP transport properties that are quantitatively consistent with the state-of-the-art knowledge.