Rob Howley, standing in as coach while Warren Gatland is on British and Irish Lions duty, made the announcement when naming a 36-man squad that included seven uncapped players.
The 31-year-old Jones, who captains the Ospreys, has led Wales on five occasions in Warburton's absence and skippered the Lions to their series-clinching third test win over Australia in 2013 when his compatriot was injured.
“It is an honour to select Alun Wyn as captain. His vast experience as a player and a leader will help drive this squad forward and I believe he will flourish in the role," Howley said in a statement.
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"Sam has led Wales more times than any other captain and had great success in the role, however we want him to concentrate on his game and to be the best player he can be. He agrees this is the best way forward."
Five of the seven uncapped players - Olly Cracknell, Thomas Young, Owen Williams, Ashton Hewitt and Steffan Evans - feature in the senior squad for the first time while Rory Thornton and Aled Davies have been in squads but are yet to play.
“There is a flavour of freshness too in the squad, with seven uncapped players deserving their opportunity and it will be exciting to see how they perform in the international set-up," Howley said.
Wales, runners-up to England last year, start their Six Nations campaign away to Italy on Feb. 5.
“It is shaping up to be another great Six Nations," Howley said.
"We have the all important carrot of Rugby World Cup seedings on the horizon post-tournament and that is an important target for us, especially as we welcome the World’s number two (England) and number four (Ireland) ranked sides to Principality Stadium over the coming months."
Wales squad
Forwards:Scott Andrews (Cardiff Blues) (13 Caps)Nicky Smith (Ospreys) (7 Caps)Rob Evans (Scarlets) (12 Caps)Rhodri Jones (Ospreys) (14 Caps)Tomas Francis (Exeter Chiefs) (17 Caps)Samson Lee (Scarlets) (29 Caps)Kristian Dacey (Cardiff Blues) (3 Caps)Ken Owens (Scarlets) (45 Caps)Scott Baldwin (Ospreys (28 Caps)Jake Ball (Scarlets) (21 Caps)Alun Wyn Jones (Ospreys) (105 Caps)Rory Thornton (Ospreys) (Uncapped)Luke Charteris (Bath Rugby) (71 Caps)Cory Hill (Newport Gwent Dragons) (3 Caps)James King (Ospreys) (10 Caps)Justin Tipuric (Ospreys) (46 Caps)Olly Cracknell (Ospreys) (Uncapped)Ross Moriarty (Gloucester Rugby) (12 Caps)Taulupe Faletau (Bath Rugby) (62 Caps) Sam Warburton (Cardiff Blues) (69 Caps)Thomas Young (Wasps) (Uncapped) Backs:Gareth Davies (Scarlets) (21 Caps)Rhys Webb (Ospreys) (23 Caps)Aled Davies (Scarlets) (Uncapped)Dan Biggar (Ospreys) (51 Caps)Sam Davies (Ospreys) (3 Caps)Owen Williams (Leicester Tigers) (Uncapped)Jamie Roberts (Harlequins) (86 Caps) Jonathan Davies (Scarlets) (59 Caps)Scott Williams (Scarlets) (41 Caps)Ashton Hewitt (Newport Gwent Dragons) (Uncapped)Alex Cuthbert (Cardiff Blues) (44 Caps)Steffan Evans (Scarlets) (Uncapped)George North (Northampton Saints) (65 Caps) Liam Williams (Scarlets) (38 Caps)Leigh Halfpenny (Toulon) (66 Caps)
(Editing by Ed Osmond)
