Myers (5-13) yielded six hits while walking one and striking out four. The ex-Philly won his second straight start after snapping a personal 14 game winless streak.
Lee's two-run blast in the fifth inning put the Astros up 4-1. J.D. Martinez went 3-for-4 with three runs scored for Houston.
Former longtime Astro Roy Oswalt (7-9) was saddled with the loss, yielding five runs on 11 hits over seven innings in his first visit to Minute Maid Park as a member of an opposing team.
Pete Orr got the only RBI for Philadelphia, which lost its second straight after a six-game winning streak.