Wales made the brighter start, racing into a 14-0 lead inside the opening half-hour, but Scotland responded brilliantly before the break. Tries from Ollie Blyth-Lafferty and Henry Kesterton in quick succession, both converted by Jake Dalziel, wiped out the deficit to leave the sides level at 14-14 at half-time.
Scotland carried that momentum into the second period. Skipper Joe Roberts crossed early after the restart to put his side ahead for the first time. Wales levelled before Dan Kelly added a fourth try after sustained pressure to restore Scotland's advantage. Dalziel maintained his perfect record from the tee. Scotland's defence stood firm through the closing stages despite being reduced to 13 players to see out the victory.
The win completed an excellent end to the championship for Fergus Pringle's side.
The fifth-place finish matches the achievement of the 2017 side, which produced eight future senior internationals, including Blair Kinghorn, Darcy Graham, Matt Fagerson and Stafford McDowall.
Scotland U20 head coach Fergus Pringle believes several of his current squad could reach the senior team just as quickly.
Asked if they could make the step up within two years, he replied: "Probably sooner."
He added: "But you don't want to put pressure on the guys, I think you just want to let things unfold. I think the big thing for these guys going back to their clubs like Edinburgh and Glasgow is that they go and perform really well in their clubs.
"I think a lot of them will say to you now that they've learned so much from training and playing with those senior players already.
"Who would have said this time last year, Seb [Stephen] would be playing. So there's no reason that Joe [Roberts] can't do the same.
"So I think it's just a matter of guys getting the opportunity, working hard as young pros and then just sticking in and being patient and taking their chance when they get it."
Scotland U20
15 Rory McHaffie (Edinburgh Rugby)
14 Daniel Kelly (Edinburgh Rugby)
13 Henry Kesterton (Edinburgh Rugby)
12 Alex Bryden (Glasgow Warriors)
11 Nairn Moncrieff (Edinburgh Rugby)
10 Jake Dalziel (Merchiston Castle/Newcastle Red Bulls) Vice-Captain
9 Asa Stewart-Harris (Saracens RFC)
1 Ollie McKenna (Glasgow Warriors)
2 Joe Roberts (Glasgow Warriors) Captain
3 Ollie Blyth-Lafferty (Edinburgh Rugby)
4 Alfie Blackett (Cardiff Metropolitan University)
5 Dan Halkon (Glasgow Warriors)
6 Christian Lindsay (Edinburgh Rugby)
7 Jack Utterson (Edinburgh Rugby)
8 Harvey Preston (Glasgow Hawks)
Substitutes
16 Jamie McAughtrie (Ayr RFC)
17 Jamie Stewart (Edinburgh Rugby)
18 Jackson Rennie (Glasgow Warriors)
19 Finlay Mather (Grammar Tec)
20 Oliver Finlayson Russell (University of St Andrews)
21 Matthew Fick (Edinburgh Rugby)
22 Calum Jessop (Heriots RFC)
23 Ewan Caven (Gloucester Rugby/Nottingham University)