Jones has scored ten tries in 17 caps for Scotland but his last score came in the Calcutta Cup win over England in February 2018 and he has struggled for form over the last 12 months.
Edinburgh back-row Magnus Bradbury, who missed the first three World Cup warm-up matches through injury, will also be left behind while Rory Hutchinson, who scored twice against Georgia in Tbilisi last weekend and looked to be making a late bid for a seat on the 'plane, hasn't made the final squad.
Forward pair Matt Fagerson of Glasgow Warriors and Josh Strauss, now at Bulls in South Africa, also failed to make the cut despite decent performances against the Georgians.
Stuart McInally has been named captain of the side while Townsend has named 17 forwards and 14 backs in his squad. Scotland's first match is against Ireland on September 22, followed by Samoa on September 30. They then face Russia on October 9 and Japan on October 13.
Speaking at Linlithgow Palace, where the squad was announced, Townsend said: "It's been a tough process getting down to 31 players, but we are very happy with the squad we've selected.
"We believe we’ve picked a group capable of playing our best rugby and doing this consistently throughout the tournament.
“The players have worked hard to be in the best physical shape of their careers and we know that when they play to their potential they are capable of beating any team in the world.
“There were a number of tough calls given the quality of our wider training squad, and on the close decisions we’ve looked to select players that have strong defensive attributes and are willing to out-work their opposite number.
“Some very good players have missed out on selection this time, but they know they’ll have to keep working hard because, in a World Cup, an opportunity can come around very quickly.”
Scotland's 2019 Rugby World Cup squad
Forwards: John Barclay (Edinburgh), Simon Berghan (Edinburgh), Fraser Brown (Glasgow Warriors), Scott Cummings (Glasgow Warriors), Allan Dell (London Irish), Zander Fagerson (Glasgow Warriors), Grant Gilchrist (Edinburgh), Jonny Gray (Glasgow Warriors), Stuart McInally (capt) (Edinburgh), WP Nel (Edinburgh), Gordon Reid (Ayrshire Bulls), Jamie Ritchie (Edinburgh), Blade Thomson (Scarlets), Ben Toolis (Edinburgh), George Turner (Glasgow Warriors), Hamish Watson (Edinburgh), Ryan Wilson (Glasgow Warriors).
Backs: Darcy Graham (Edinburgh), Chris Harris (Gloucester), Adam Hastings (Glasgow Warriors), Stuart Hogg (Exeter Chiefs), George Horne (Glasgow Warriors), Pete Horne (Glasgow Warriors), Sam Johnson (Glasgow Warriors), Blair Kinghorn (Edinburgh), Greig Laidlaw (Clermont Auvergne), Sean Maitland (Saracens), Ali Price (Glasgow Warriors), Finn Russell (Racing 92), Tommy Seymour (Glasgow Warriors), Duncan Taylor (Saracens).