Marquis (4-2) logged a third victory in three starts, taming the Marlins on five hits. The veteran right-hander issued one walk and struck out three for the Padres, who allowed a total of one run to the Marlins in the series.
Huston Street struck out two during a 1-2-3 ninth, racking up his eighth save.
San Diego scored the game's only run in the sixth inning.
Yonder Alonso then followed with a sacrifice fly to provide the winning margin.
Nolasco (2-4) absorbed the hard-luck loss, yielding just the one run on four hits while walking one and striking out nine.