Manning has not missed a start in his 12-year career, a streak that is at 201 including playoff games. He was listed as a limited participant one other time this season.
Manning was one of 25 players and 13 starters on the Colts' long list of injuries.
Left tackle Charlie Johnson (foot) was also limited at practice. Four starters did not practice at all: wide receiver Reggie Wayne (foot), defensive end Dwight Freeney (abdomen), safety Antoine Bethea (foot) and cornerback Kelvin Hayden (knee).
Seven starters on the list did not miss any practice time.
Indy visits Houston on Sunday with a chance to clinch the AFC South title.