The A's were trailing 5-2 in the third inning when they began a comeback, scoring runs on a Brandon Moss double and an error by second baseman Matt Carpenter.
In the next frame, Chris Young led off with a double against Cards starter Jake Westbrook, and after Seth Smith popped out, Lowrie belted a 1-0 pitch off the facing of the grandstand in right field, putting Oakland ahead to stay.
Josh Donaldson also homered for the A's, who stayed one-half game behind American League West-leading Texas with their second victory in three contests against St. Louis.
Tommy Milone (7-7) collected the decision despite yielding five runs (four earned) on seven hits over six innings. He walked two and fanned five.
Westbrook (4-3) was lit up for six runs on 10 hits over just four frames.
Carlos Beltran went 3-for-4 with a two-run homer for the Cardinals.
Carpenter supplied three hits, including a solo shot, and Allen Craig also went deep for St. Louis.