Kandji, 26, has played 57 regular season matches over five seasons in MLS. He was only able to make 12 appearances, including three in the playoffs, last season after tearing his ACL in the 2010 MLS Cup final.
"I've always liked Macoumba as a player," said Houston coach Dominic Kinnear. "His athleticism and good play to goal will be a good fit for our team."
Houston will play its first seven games on the road this season before opening BBVA Compass Stadium on May 12 against D.C. United.