Warburton replaces Justin Tipuric in the No7 shirt, while James is called up in place of double Lion Gethin Jenkins, who misses out with a calf injury he picked up in the win over Italy.
Jones is named ahead of Andrew Coombs, with his experience meaning the Dragons newcomer drops to the bench despite three outstanding displays so far in his debut international season.
Ospreys second row Jones featured in all three Tests when the Lions toured South Africa four years ago but hasn't started a game for his country since the first match of the autumn series after undergoing shoulder surgery.
Clubmate Ryan Jones will continue to skipper the side despite the return of Warburton who began the tournament as one of the favourites for the Lions captaincy this summer.
Warburton sat out the victory in France with a stinger injury to his shoulder and then had to make do with a place on the bench in Rome just over a week ago but has now been recalled by interim head coach Rob Howley.
"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, who will be part of Warren Gatland's tour party when the Lions head Down Under.
"It's disappointing for Gethin to miss out but Paul has impressed and made an impact in each game he has played.
"Ryan has led the team to two wins and deserves to captain the side against Scotland.
"We have had two good, hard fought away victories but we know will have to be at our best again to come away from Murrayfield with the result.
"We have spoken a lot about momentum in this tournament and we go into the game with two wins under our belt but Scotland are in the same position."
Howley has made a further change to his bench as Ryan Bevington replaces Craig Mitchell, while Blues prop Scott Andrews steps up in place of the promoted James and Tipuric and Coombs swap places with Warburton and Jones.
Wales (versus Scotland, Murrayfield, Saturday 2.30pm)
Leigh Halfpenny (Cardiff Blues); Alex Cuthbert (Cardiff Blues), Jonathan Davies (Scarlets), Jamie Roberts (Cardiff Blues), George North (Scarlets), Dan Biggar (Ospreys), Mike Phillips (Bayonne); Paul James (Bath), Richard Hibbard (Ospreys), Adam Jones (Ospreys), Alun Wyn Jones (Ospreys), Ian Evans (Ospreys), Ryan Jones (Ospreys, capt), Sam Warburton (Cardiff Blues), Toby Faletau (Dragons)
Replacements: Ken Owens (Scarlets), Ryan Bevington (Ospreys), Scott Andrews (Cardiff Blues), Andrew Coombs (Dragons), Justin Tipuric (Ospreys), Lloyd Williams (Cardiff Blues), James Hook (Perpignan), Scott Williams (Scarlets)