A central issue in the quest to understand the superconductivity in cuprates is the nature and origin of the pseudogap state, which harbours anomalous electronic states such as Fermi arc, charge density wave (CDW), and $d$-wave superconductivity. A fundamentally important, but long-standing controversial problem has been whether the pseudogap state is a distinct thermodynamic phase characterized by broken symmetries below the onset temperature $T^*$. Electronic nematicity, a fourfold ($C_4$) rotational symmetry breaking, has emerged as a key feature inside the pseudogap regime, but the presence or absence of a nematic phase transition and its relationship to the pseudogap remain unresolved. Here we report thermodynamic measurements of magnetic torque in the underdoped regime of orthorhombic YBa$_2$Cu$_3$O$_y$ with a field rotating in the CuO$_2$ plane, which allow us to quantify magnetic anisotropy with exceptionally high precision. Upon entering the pseudogap regime, the in-plane anisotropy of magnetic susceptibility increases after exhibiting a distinct kink at $T^*$. Our doping dependence analysis reveals that this anisotropy is preserved below $T^*$ even in the limit where the effect of orthorhombicity is eliminated. In addition, the excess in-plane anisotropy data show a remarkable scaling behaviour with respect to $T/T^*$ in a wide doping range. These results provide thermodynamic evidence that the pseudogap onset is associated with a second-order nematic phase transition, which is distinct from the CDW transition that accompanies translational symmetry breaking. This suggests that nematic fluctuations near the pseudogap phase boundary have a potential link to the strange metallic behaviour in the normal state, out of which high-$T_c$ superconductivity emerges.
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