The Cardinals have won two of the first three outings in the four-game series.
It was a 1-1 game heading into the sixth, but Matt Holliday opened that inning with a single. Allen Craig reached on a fielder's choice grounder that erased Holliday at second and Molina followed with his fifth homer of the season.
That blast came off starter Edwin Jackson (3-9), who then hit Jon Jay with a pitch. Jackson was relieved by Carlos Villanueva, who allowed a single to Daniel Descalso and a run-scoring base hit by Pete Kozma.
Jake Westbrook, in his second start since returning from the disabled list, gave up an unearned run on two hits over seven innings to get the win.
Westbrook (3-2) had given up five runs in his previous outing after missing a month of action with elbow inflammation.
Edward Mujica needed just eight pitches to complete a perfect ninth inning that gave him his 21st save.