Roberto Martinez's side lifted the trophy for the second time by beating current holders Spain, coming out on top 5-3 in a penalty shootout, following a 2-2 draw.
Fernandes kept his customary composure to effortlessly slot his spot-kick past Unai Simon, with Alvaro Morata's miss later in proceedings proving pivotal, Diogo Costa saving to set up the winning effort by Ruben Neves.
Fernandes did find the net soon after the restart in normal time, firing past Simon from an angle, only for the goal to be ruled out for offside.