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We present a first-principles study of the low-temperature rhombohedral phase of BaTiO$_3$ using Hubbard-corrected density-functional theory. By employing density-functional perturbation theory, we compute the onsite Hubbard $U$ for Ti($3d$) states and the intersite Hubbard $V$ between Ti($3d$) and O($2p$) states. We show that applying the onsite Hubbard $U$ correction alone to Ti($3d$) states proves detrimental, as it suppresses the Ti($3d$)-O($2p$) hybridization and drives the system towards a cubic phase. Conversely, when both onsite $U$ and intersite $V$ are considered, the localized character of the Ti($3d$) states is maintained, while also preserving the Ti($3d$)-O($2p$) hybridization, restoring the rhombohedral phase of BaTiO$_3$. The generalized PBEsol+$U$+$V$ functional yields good agreement with experimental results for the band gap and dielectric constant, while the optimized geometry is slightly less accurate compared to PBEsol. Zone-center phonon frequencies and Raman spectra are found to be significantly influenced by the underlying geometry. PBEsol and PBEsol+$U$+$V$ provide satisfactory agreement with the experimental Raman spectrum when the PBEsol geometry is used, while PBEsol+$U$ Raman spectrum diverges strongly from experimental data highlighting the adverse impact of the $U$ correction alone in BaTiO$_3$. Our findings underscore the promise of the extended Hubbard PBEsol+$U$+$V$ functional with first-principles $U$ and $V$ for the investigation of other ferroelectric perovskites with mixed ionic-covalent interactions.