The Athletics won their fourth in a row, the longest current streak in the American League.
Oakland faced a 3-1 deficit heading into the sixth, which Lowrie began with a homer to right.
A fielding error by Houston shortstop Ronny Cedeno later prolonged the inning and Oakland capitalized by loading the bases and scoring runs on singles from Josh Donaldson, Derek Noris and Eric Sogard.
That outburst allowed Bartolo Colon (1-0) to pick up the win. He gave up three runs, all of them on a homer by Jason Castro, on eight hits over six innings. Grant Balfour struck out one in a perfect ninth for his first save.
Bud Norris (1-1) took the loss, although only two of the five runs he allowed were earned. Norris was the winning pitcher in Houston's opening game of the season and the Astros have lost their next four.