Fuller appeared to injure his hamstring after making a catch on the second play of the Texans' opening drive. He was announced as questionable to return early in the first quarter, and then ruled out at the start of the second half.
The wide receiver was limited in practice on Wednesday with injuries to his calf and oblique, but was a full participant in practice on Thursday and Friday.
Fuller had one catch for six yards against the Colts. He has 34 catches for 450 yards and three touchdowns this season.
Texans wide receiver Kenny Stills is active against the Colts after missing the past two games with a hamstring injury.