In spring 2012 CERN provided two weeks of a short bunch proton beam dedicated to the neutrino velocity measurement over a distance of 730 km. The OPERA neutrino experiment at the underground Gran Sasso Laboratory used an upgraded setup compared to the 2011 measurements, improving the measurement time accuracy. An independent timing system based on the Resistive Plate Chambers was exploited providing a time accuracy of $\sim$1 ns. Neutrino and anti-neutrino contributions were separated using the information provided by the OPERA magnetic spectrometers. The new analysis profited from the precision geodesy measurements of the neutrino baseline and of the CNGS/LNGS clock synchronization. The neutrino arrival time with respect to the one computed assuming the speed of light in vacuum is found to be $\delta t_\nu \equiv TOF_c - TOF_\nu= (0.6 \pm 0.4\ (stat.) \pm 3.0\ (syst.))$ ns and $\delta t_{\bar{\nu}} \equiv TOF_c - TOF_{\bar{\nu}} = (1.8 \pm 1.4\ (stat.) \pm 3.2\ (syst.))$ ns for $\nu_{\mu}$ and $\bar{\nu}_{\mu}$, respectively. This corresponds to a limit on the muon neutrino velocity with respect to the speed of light of $-1.8 \times 10^{-6} < (v_{\nu}-c)/c < 2.3 \times 10^{-6}$ at 90% C.L. This new measurement confirms with higher accuracy the revised OPERA result.