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.
Boston schools pull out free condoms over wrapping complaints
Millions of Getty images now available for free via embed tool