The strongly correlated system Ho11B12 with boron sublattice Jahn-Teller instability and nanoscale electronic phase separation (dynamic charge stripes) was studied in detail by inelastic neutron scattering (INS), magnetometry and heat capacity measurements at temperatures in the range 3-300 K. From the analysis of registered INS spectra, we determined parameters of the cubic crystal field at holmium sites, B4=- 0.333 meV and B6= -2.003 meV (in Stevens notations), with an unconventional large ratio B6/B4 pointing on the dominant role of conduction electrons in the formation of a crystal field potential. The molecular field in the antiferromagnetic state, Bloc = (1.75+- 0.1) T has been directly determined from the INS spectra together with short-range order effects detected in the paramagnetic state. A comparison of measured magnetization in diluted Lu0.99Ho0.01B12 and concentrated HoB12 single crystals showed a strong suppression of Ho magnetic moments by antiferromagnetic exchange interactions in holmium dodecaboride. To account explicitly for the short-range antiferromagnetic correlations, a self-consistent holmium dimer model was developed that allowed us to reproduce successfully field and temperature variations of the magnetization and heat capacity in the cage-glass phase of HoB12 in external magnetic fields.