With Sheffield United beaten earlier in the day, the table-topping Canaries took full advantage to stretch the gap to now-second-placed Leeds United thanks to Hernandez's fine strike.
Norwich enjoyed the best chances of the first half and Darren Randolph twice frustrated Teemu Pukki with smart stops from the in-form forward.
Boro almost broke the deadlock shortly after the interval when Daniel Ayala crashed a header from Ryan Shotton's long throw against the foot of the post, but the breakthrough came at the other end after 54 minutes.
Hernandez cut inside from the left and drilled a low effort inside Randolph's near post to set Norwich up for a late defensive showing.
Despite a couple of scrambles in Tim Krul's box in the closing stages, Boro could not find an equaliser and remains in eighth place, having dropped out of the play-off places after results elsewhere.