The square-lattice quantum Heisenberg antiferromagnet displays a pronounced anomaly of unknown origin in its magnetic excitation spectrum. The anomaly manifests itself only for short wavelength excitations propagating along the direction connecting nearest neighbors. Using polarized neutron spectroscopy, we have fully characterized the magnetic fluctuations in the model metal-organic compound CFTD, revealing an isotropic continuum at the anomaly indicative of fractional excitations. A theoretical framework based on the Gutzwiller projection method is developed to explain the origin of the continuum at the anomaly. This indicates that the anomaly arises from deconfined fractional spin-1/2 quasiparticle pairs, the 2D analog of 1D spinons. Away from the anomaly the conventional spin-wave spectrum is recovered as pairs of fractional quasiparticles bind to form spin-1 magnons. Our results therefore establish the existence of fractional quasiparticles in the simplest model two dimensional antiferromagnet even in the absence of frustration.