Coach Warren Gatland took the bold decision to introduce the pair for James Hook and Mike Phillips after Wales’ lead had been pegged back to 17-15 with 20 minutes left.
Baseball teams have pitchers whose speciality is to close out a victory – and Jones played that role to perfection in his first appearance for Wales since the World Cup.
Jones’ steadying arm kept Wales in Scottish territory and built the platform for Shane Williams to provide the telling breakthrough with an electric break and extraordinary finish in the corner.
Replays later suggested his foot may have been in touch but the Italian television match official Carlo Damasco was satisfied, and Wales had their second victory of the campaign.
They will travel to Dublin to face Ireland, Gatland’s former employers, in a month’s time with a shot at the Triple Crown.
But before then, Italy visit the Millennium Stadium a week on Saturday and Gatland is prepared to ring the changes in a constant drive for perfection. Asked whether there is a strong temptation to start with Peel and Jones, Gatland said: “Yes there is. That is a fair point.
“Both are really experienced and you have to keep in mind that if you do pick up one or two injuries then you have to make sure you have given the guys in your squad some game time.
“I thought Dwayne was a little off the pace when he came on. Stephen Jones did what was required and really showed a lot of maturity. It was his job to bring us home and he did that really well.
“I felt we needed some experience in the last 20 minutes, guys who had been around for a while. Stephen did that magnificently, a couple of crucial goal kicks took us to the line.
“Some guys made a mark off the bench – Gethin Jenkins, Matthew Rees, Gareth Delve and Stephen Jones – and the thinking at the moment is to make a few changes against Italy.
“I’m not talking wholesale changes but giving players who have been on the bench an opportunity to start.”
Gatland’s decisive substitutions will re-ignite the Jones-Hook debate, which began before the World Cup after the Ospreys youngster made such an emphatic start to his Test career.
Jones, who was not used during the win at Twickenham, said: “I was just delighted to get back on the pitch and try and express myself. This is by far the most competitive Welsh squad I can remember. We have two wins but as players we will not get carried away. We need to up our game.
“I am sure there will be quite a few areas the coaches won’t be happy about and they won’t hold back. They want us to develop as a team and as individuals.”
Gatland and Shaun Edwards lauded Wales’ defence, which kept Scotland out at the death even when the game was won.
A side that leaked points during the World Cup has now conceded just once – to a cross-kick aimed at the giant Lesley Vainikolo in the win over England – in two matches.
But what did concern Gatland about yesterday’s performance was Wales’ inability to shake off a Scotland side which created little but capitalised on “stupid penalties” to remain in touch.
Wales should have buried Scotland after opening a 10-3 lead following Williams’ first try, and then again after Hook had glided over to secure a 17-9 advantage.
But Chris Paterson converted five penalties in yet another faultless kicking display to pass Gavin Hastings record as Scotland’s leading points scorer in Five/Six Nations history.
“When you get that amount of possession and territory, you need to be more ruthless in putting teams away,” said Gatland, who was critical of Scotland’s approach.
“If we have ambitions of being a side that can compete with the best in the world, then we have to take the chances that are presented to us. We didn’t do that and we have to keep working on our attention to detail.
“But the attitude is fantastic. If we continue with the hard work we will get there.’’
Wales scorers: Tries: S. Williams 2, Hook. Cons: Hook 2, S. Jones. Pens: Hook, S. Jones 2.
Byrne, Roberts, Shanklin, Henson, S. Williams, Hook, Phillips, D. Jones, Bennett, A. Jones, Gough, Evans, Thomas, M. Williams, R. Jones.
Replacements: Parker for Shanklin (71), S. Jones for Hook (58), Peel for Phillips (58), Jenkins for D. Jones (54), Rees for Bennett (58), D. Jones for Gough (73), Delve for R. Jones (62).
Scotland scorers: Pens: Paterson 5.
Southwell, Walker, De Luca, Henderson, Paterson, Parks, Blair, Jacobsen, Ford, Murray, Hines, Hamilton, White, Brown, Barclay.
Replacements: Danielli for Walker (74), Cusiter for Blair (73), Thomson for Ford (73), MacLeod for Hines (62), Hogg for White (32).
Ref: Bryce Lawrence.