The Phillies had their season-best, seven-game winning streak snapped by a team that is only two losses away from having 100 of them for the season.
Philadelphia took a 4-0 lead through three innings, but Houston got back in it on a three-run homer from Matt Dominguez in the fourth.
Lowrie's two-run double then gave the Astros the lead in the eighth and he later scored on a base hit by Brandon Barnes. Houston has won four times in its last seven games.
Wesley Wright (1-2) recorded the final two outs in the eighth to collect his first win in two years and only the ninth of his five-year career. Wilton Lopez gave up a leadoff single in the ninth, but retired the next three batters for his fifth save.
Phillippe Aumont (0-1), the fifth of six Philadelphia pitchers, took the loss. It was his first major league decision and came in his 10th appearance.