Wales had most of the early territory and possession and went ahead with a penalty before Tommy Allan replied with a three-pointer for Scotland.
Scotland, skippered by Glasgow's Jonny Gray, went ahead on 25 minutes with Shawn Muir touching down after a great drive from the home forwards.
Tommy Allan added the extras to give the Scots a 10-3 lead but just two minutes later a wayward Scottish pass was intercepted and Wales went over for the try.
There was no conversion so the Scots still lead but that wasn't to last long as two tries in the final three minutes of the half saw Wales go into the interval 22-10 ahead.
Wales increased their lead 5 minutes into the second period with another penalty and worse was to come for the Scots as they conceded another try after coughing up possession in their own 22.
The home team couldn't take advantage of a Welsh yellow card and with the teams back to 15 players the Scots conceded a penalty try after a series of scrums to take the score to 37-10.
Another yellow card for the visitors followed but it didn't stop them scoring the try of the match after a breakout from their own line to take the score to 42-10.
With two minutes left Glasgow's Adam Ashe went over for a try with Allan adding the conversion.
* The Scotland Club International team beat their Irish counterparts 30-18 at Millbrae this evening.