Receiver Marvin Harrison (knee), running back Joseph Addai (shoulder), safety Bob Sanders (ribs) and linebacker Freddy Keiaho (concussion) were back in the starting lineup for the Colts after missing the Tampa Bay game two weeks ago.
Jones was inactive for Jacksonville's game at Denver earlier this season, a move that raised questions about his future with the franchise.
His agent, Alan Herman, criticized the decision and said he would seek a trade if it continued.
But Jaguars coach Jack Del Rio defended the move, even though he had earlier ripped Jones about his on-the-field body language. Del Rio indicated Jones takes plays off and pouts when he doesn't get the ball.
Jones, the 18th overall draft pick in 2005, has eight catches for 74 yards this season.
These division rivals know each other very well and this will be a very important game in the AFC South race. The Colts are coming off a bye and will be well-rested, while the Jaguars are coming off a physical pounding of Houston that put them at 4-1 and in the thick of the playoff race.
This is a fascinating contrasts in styles. Indianapolis will try to out-scheme Jacksonville with QB Peyton Manning's pre-snap adjustments and movement, along with its small but athletic defense, while Jacksonville simply will try to punch the Colts in the mouth and dominate them physically on both sides of the ball. As good as Indianapolis is, it still will need its "A game" to win in Jacksonville.