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We present a comprehensive experimental investigation of Yb magnetic dimers in Yb$_{0.04}$Y$_{0.96}$AlO$_3$, an Yb-doped Yttrium Aluminum Perovskite (YAP) YAlO$_3$ by means of specific heat, magnetization and high-resolution inelastic neutron scattering (INS) measurements. In our sample, the Yb ions are randomly distributed over the lattice and $\sim 7$\% of Yb ions form quantum dimers due to nearest-neighbor antiferromagnetic coupling along the $c$-axis. At zero field, the dimer formation manifests itself in an appearance of an inelastic peak at $Δ\approx 0.2$~meV in the INS spectrum and a Schottky-like anomaly in the specific heat. The structure factor of the INS peak exhibits a cosine modulation along the $L$ direction, in agreement with the $c$-axis nearest-neighbor intra-dimer coupling. A careful fitting of the low-temperature specific heat shows that the excited state is a degenerate triplet, which indicates a surprisingly small anisotropy of the effective Yb-Yb exchange interaction despite the low crystal symmetry and anisotropic magnetic dipole contribution, in agreement with previous reports for the Yb parent compound, YbAlO$_3$ [arXiv:1904.11513, arXiv:1902.04112], and in contrast to Yb$_2$Pt$_2$Pb [arXiv:1606.01309, arXiv:1907.01067]. The obtained results are precisely reproduced by analytical calculations for the Yb dimers.