We investigated the low-energy incommensurate (IC) magnetic fluctuations in Sr$_2$RuO$_4$ by the high-resolution inelastic neutron scattering measurements and random phase approximation (RPA) calculations. We observed a spin resonance with energy of $hbaromega_text{res}=0.56$~meV centered at a characteristic wavevector $mathbf{Q}_text{res}=(0.3, 0.3, 0.5)$. The resonance energy corresponds well to the superconducting gap $2Delta=0.56$~meV estimated by the tunneling spectroscopy. The spin resonance shows the $L$ modulation with a maximum at around $L = 0.5$. The $L$ modulated intensity of the spin resonance and our RPA calculations indicate that the superconducting gaps regarding the quasi-one-dimensional $alpha$ and $beta$ sheets at the Fermi surfaces have the horizontal line nodes. These results may set a strong constraint on the pairing symmetry of Sr$_2$RuO$_4$. We also discuss the implications on possible superconducting order parameters.