The 38-year-old Farnsworth was released by the Mets on May 14 after posting a 3.18 ERA with three saves in 19 appearances this season.
Terms of the deal were not released.
Houston optioned right-hander Paul Clemens to Triple-A Oklahoma City to make room for Farnsworth on the roster. Clemens has a 4.08 ERA in eight appearances for Houston this season.
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