Jones, who turns 37 at the beginning of next month, will leave the Coral Windows Stadium after Bantams boss Phil Parkinson elected not to offer the City skipper a new deal with the club.
The Birkenhead-born midfielder will depart the Bantams having made exactly 100 appearances for City over the past two seasons, 93 of which came from the start.
In his 93 starts for the club, Jones was captain on each occasion.
Having signed for City from Rochdale in June 2012, Jones memorably captained Parkinson's men all the way through to the Capital One Cup Final and promotion into League 1 in his first season at the Coral Windows Stadium.
The all-action performer was also named as the club's Player of the Year for that season.
Jones finishes his career with the Bantams having led them to an eleventh placed finish in their first season back in League 1, scoring six goals in the process.
Speaking about Jones and his successful time at City, Parkinson was quick to heap praise on his departing skipper.
He said: "I had a meeting with Gaz (Gary Jones) today (Friday) and I told him that he wasn't going to be offered a new contract.
"I would like to take this opportunity to thank Gaz for his enormous contribution to the club over the last two seasons.
"Two years ago, we went out in search for players who had the right mentality and character to get the club going again. Gary Jones typified absolutely everything we were looking for.
"He has been a superb role model for our younger players and he has put his heart and soul into the club every single day for the last two years. I cannot speak highly enough of him both as a person and as a football player.
"I wish him all the very best for the future, and I am sure the fans will be quick to do likewise.
"I am confident that there are still many more games left in Gary before he finally decides to hang up his boots."