The Scots capitalised on the ill-discipline of a Welsh team - scrum-half Logan Franklin was shown a 20-minute red card for an illegal ruck clearout and lock Tom Cottle then received a permanent red card for a dangerous and late challenge.
Scotland skipper Freddy Douglas went over for two tries while there were further scores for wing Nairn Moncrieff and full-back Jack Brown end two years without a win in the U20 Six Nations
Prop Ioan Emanuel and hooker Harry Thomas scored tries for Wales.