In exchange, the Rockies sent minor league pitchers Wes Musick and Jonnathan Aristil to Houston in a deal that was announced Thursday.
Lindstrom has made at least 50 appearances in all four of his seasons in the majors. He had a team-high 23 saves for the Astros in 2010, finishing 2-5 with a 4.39 ERA.
A converted position player, Aristil spent time at three different levels in the Rockies' organization last season, winding up at Triple-A Colorado Springs where the right-hander threw two scoreless innings.
The left-handed Musick started 23 games at Single-A Asheville, turning in an 8-7 record with a 4.05 ERA.