Scutaro's two-run single in the fourth inning put the Giants ahead 5-1 and his RBI hit in the sixth gave San Francisco a 7-3 advantage.
Brandon Belt went 2-for-3 with a solo homer and three runs scored, while Hunter Pence delivered a sacrifice fly as the Giants claimed their second NL West crown in three years.
Madison Bumgarner (16-10) earned the victory, allowing three runs (two earned) on five hits over 5 2/3 innings. He walked one and struck out six as the Giants notched their sixth straight win.
Andrew Werner (2-2) was tagged for five runs on six hits in a 3 2/3-inning start for the Padres.
Yonder Alonso knocked a two-run homer and Chase Headley drove in two runs for San Diego.