Jones, installed as skipper in Paris after Warburton undertook the job against Ireland, holds onto the captaincy despite Warburton's recall, while in two other changes, prop Paul James and lock Alun Wyn Jones are both selected.
James will win his 44th test cap at Murrayfield and comes in to the side after Gethin Jenkins failed to recover from a calf injury picked up in the victory to Italy.
Jones, who came off the bench in Italy following a shoulder problem, comes in for Andrew Coombs, who has impressed in the second row having made his debut against Ireland.
For the fourth match running, interim head coach Rob Howley has named an unchanged back line.
"We are bringing in a wealth of experience with Alun Wyn and Sam and they both performed well off the bench in Rome," said Howley.
"Ryan has led the team to two wins and deserves to captain the side against Scotland."
Wales and Scotland go into Saturday's match level on points in the RBS 6 Nations table with two victories apiece and the visitors will be looking for their fifth successive away victory in the tournament, a feat they haven't achieved before.
15 Leigh Halfpenny (Cardiff Blues)
14 Alex Cuthbert (Cardiff Blues)
13 Jonathan Davies (Scarlets)
12 Jamie Roberts (Cardiff Blues)
11 George North (Scarlets)
10 Dan Biggar (Ospreys)
9 Mike Phillips (Bayonne)
1 Paul James (Bath)
2 Richard Hibbard (Ospreys)
3 Adam Jones (Ospreys)
4 Alun Wyn Jones (Ospreys)
5 Ian Evans (Ospreys)
6 Ryan Jones (Ospreys)
7 Sam Warburton (Cardiff Blues)
8 Toby Faletau (Newport Gwent Dragons)
Ken Owens (Scarlets)
Ryan Bevington (Ospreys)
Scott Andrews (Cardiff Blues)
Andrew Coombs (Newport Gwent Dragons)
Justin Tipuric (Ospreys)
Lloyd Williams (Cardiff Blues)
James Hook (Perpignan)
Scott Williams (Scarlets)