Lowrie hit his 15th homer of the season in his 88th game, nine more than he had with Boston a year ago in the same number of contests.
Pittsburgh has dropped four in a row as part of a late-season collapse that has taken the Pirates out of playoff contention. They climbed to 16 games over .500 in early August but are now two games below the breakeven mark.
Houston starter Edgar Gonzalez had to leave the game after 1 2/3 innings due to a strained hamstring and the win went to Fernando Rodriguez (2-10), who gave up two hits and no runs over 3 1/3.
Jeff Locke (0-2) struck out eight over five innings, but he gave up the three-run homer to Lowrie and absorbed the loss.
Locke is still looking for his first major league win after making eight starts over two seasons.