The 29-year-old bowed out due to the same ailment that has plagued him all season, according to national team coach Jose Pekerman.
"The injuries and problems Valencia has carried do not allow him to reach the form the national team needs in the World Cup," Sky Sports News quotes the Argentine-born boss as saying.
"We are forced to leave him out, considering that he will not make it in the best physical condition."
Valencia is the fourth player to be cut from Pekerman's provisional squad through injury, following America defender Aquivaldo Mosquera, Mainz midfielder Elkin Soto and Al Shabab midfielder Macnelly Torres.
Colombia face Greece, Ivory Coast and Japan in Group C.