They took the lead on only three minutes when Chris Thorman opened up a gap for Matthew Duckworth to run through from short range.
Soon after that, the game was stopped for 10 minutes following an injury to Scott Woods, son of coach Dave. He was taken to hospital with a suspected broken neck but reports after the game thankfully denied that.
Scorpions finally got on the board when Lloyd White kicked a penalty and then took the lead from an Andrew Gay try that White converted.
But York levelled when Thorman broke through from short range. Waterman missed the conversion but kicked a penalty on the hooter to put them 10-8 up.
White was given an early second-half chance to level after York were penalised for interference but he sliced the kick wide, before Liam Roach went over for a try and this time, White's two points were good.
York struck back when Jack Lee did well to reach out to place the ball over the whitewash. Ratcliffe converted.
Lloyd White levelled things for Scorpions with four minutes to go after kicking a penalty but the final word came from York with a minute to go after Danny Ratcliffe did likewise to secure the win.
South Wales: Kear, Murphy, Roets, Williams, Bateman, Bromilow, Gay, Roach, White, Dudson, Davis, Mills, A. James. Substitutes: Parry, Dallimore, McLocklan, Burke.
York: Ratcliffe, Reittie, Esders, Waterman, Wilson, Thorman, Woods, Freer, Lee, Benson, Ross, Duckworth, Hardbottle. Substitutes: Mitchell, Stamp, Stearman, Dinsdale.
Referee: C Leatherbarrow (RFL)