He was acquired from Boston in a trade in December that saw Houston also get pitcher Kyle Weiland from reliever Mark Melancon.
Lowrie appeared in a career-high 88 games last season and batted .252 with six home runs and 36 runs batted in. He played at every infield position in 2011.
Over four seasons in the majors, all with Boston, the 27-year-old has played in 256 games and has batted .252 with 19 home runs and 117 RBI.
With his signing, the team has all arbitration eligible players under contract for the 2012 season.