The Pirates were trailing 2-1 in the fifth when McCutchen's two-run shot vaulted the Bucs into the lead to stay, and Jones followed with a solo shot off Brewers starter Michael Fiers (1-1).
James McDonald (5-2) earned the victory by allowing only one earned run on four hits over six innings. The right-hander surrendered one walk and struck out eight in the win.
Fiers, making his second major league start, gave up four runs on eight hits in a five-inning effort. The rookie right-hander also fanned eight in the loss.
Nyjer Morgan, Brooks Conrad and Martin Maldonado each smacked a bases-empty homer for Milwaukee.