The 36 squad members include uncapped Wasps flanker Thomas Young and Newport Gwent Dragons wing Ashton Hewitt.
Injured Ospreys wing Keelan Giles has not been selected while George North, Jamie Roberts and Taulupe Faletau continue as "wildcard" picks.
Wales coach Rob Howley said: "It's 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.
"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.
"We had conversations during and since the autumn with Sam. No player is guaranteed their place in an international team and we want Sam to be playing his very best rugby and he agrees this is the best way forward."
North, Roberts and Faletau fall under the so-called "Gatland's Law" which limits the number of Welsh exiles Wales can select.
Ospreys captain Jones, 31, has often deputised for Cardiff Blues' Warburton, including in the 2013 British and Irish Lions' third Test win over Australia when the latter was injured.
Young has impressed this season under his father and former Wales prop and captain Dai at Wasps.
Along with Ospreys' Justin Tipuric and Gloucester flanker Ross Moriarty, Young is putting pressure on 28-year-old Warburton for a starting spot.
Ospreys scrum-half Rhys Webb makes the squad having not played since injuring an ankle in Wales' November defeat by Australia.
The uncapped contingent are Ospreys flanker Olly Cracknell, lock team-mate Rory Thornton, Leicester fly-half Owen Williams, Scarlets wing Steffan Evans, Hewitt and Young.
In the absence of veteran record Wales cap-holder prop Gethin Jenkins (calf), Wales welcome back Scarlets loose-head Rob Evans after injury.
Jenkins, 36, has amassed 129 Wales caps and five more for the Lions.

Wales 2017 Six Nations squad
Forwards: Scott Andrews (Cardiff Blues), Nicky Smith (Ospreys), Rob Evans (Scarlets), Rhodri Jones (Ospreys), Tomas Francis (Exeter Chiefs), Samson Lee (Scarlets), Kristian Dacey (Cardiff Blues), Ken Owens (Scarlets), Jake Ball (Scarlets), Alun Wyn Jones (Ospreys), Rory Thornton (Ospreys), Luke Charteris (Bath Rugby), Cory Hill (Newport Gwent Dragons), James King (Ospreys), Justin Tipuric (Ospreys), Olly Cracknell (Ospreys), Ross Moriarty (Gloucester Rugby), Taulupe Faletau (Bath Rugby), Sam Warburton (Cardiff Blues), Thomas Young (Wasps).
Backs: Gareth Davies (Scarlets), Rhys Webb (Ospreys), Aled Davies (Scarlets), Dan Biggar (Ospreys), Sam Davies (Ospreys), Owen Williams (Leicester Tigers), Jamie Roberts (Harlequins), Jonathan Davies (Scarlets), Scott Williams (Scarlets), Ashton Hewitt (Newport Gwent Dragons), Alex Cuthbert (Cardiff Blues), Steffan Evans (Scarlets), George North (Northampton Saints), Liam Williams (Scarlets) Leigh Halfpenny (Toulon).

Six Nations: Italy v Wales
Date: Sunday, 5 February Venue: Stadio Olimpico, Rome Kick-off: 14:00 GMT
Coverage: Live on S4C, BBC Radio Wales, BBC Radio Cymru & BBC Sport website and BBC Sport app, plus live text commentary