Scotland resumed as they had finished the half, Gallagher with the initial line break before the ball was trucked up through the forwards and eventually out to Thomson for the try.
But more drama ensued as Rachel McLachlan was shown to have obstructed the defence in the build-up much to the frustration of the 4,000 home crowd.
But Wales remained their own worst enemy, Kayleigh Powell, playing in a new position at centre, was caught in possession which allowed Thomson to hoof the ball downfield. Wales looked to have scrambled but spilled possession under the pressure of the chase which allowed Orr to pick up the ball and sprint clear to the line.
Wales then went on a rare attack with Chloe Rollie driven back over her own try line, but the tackle by Evans was high and she was shown a second yellow having only just returned to the field.
Galvanised by the dismissal, Wales kept plugging away and this time it was Scotland who were under the TMO microscope with Gallagher shown a card for a dangerous cleanout.
Wales attacked from the line-out and there was no stopping the maul with Fleming a deserved try-scorer having been at the heart of everything.
Bevan reduced the deficit to just three points with a successful conversion to send the travelling fans wild as the rain poured down.
But as conditions worsened, Scotland re-took control of the game and it was a brilliant passage of play which led to a try for Bartlett.
Orr put Wales on the backfoot with another superb line-break, showing no signs of rust after a long injury lay-off, while Thomson was hauled down by Joyce-Butchers, but Scotland showed good patience which allowed the replacement prop to go over to give Scotland some breathing space once more.
But Wales were not done, Powell had been just a roll away from crossing for a try, but Wales came again off the maul and it was the returning Pyrs who announced her arrival with a crucial try.
Scotland managed the game well in the dying minutes as Wales tried desperately to win back possession, but as the clock turned red the ball was sent high into the crowd to start the celebrations.
Wales do however travel home with deserved losing bonus-point.
