But the hosts held their nerve to progress. Saints missed two spot-kicks, with Anthony Moore saving one effort, to put AFC Flixton in the box-seat.
And even though Jordan Hume was denied, teammates Adam Wilson, Jonny Alexander, Dan Garmen and Rafi Leeker all kept their cool.
Joint-manager Stuart Delmonte told JC Sport: "It was a great win and it sets up a really interesting tie. This will be good test of how far we have progressed as a side this season.
"We will look to take the game to them and see what happens.
"We know we will be underdogs but we have shown we can beat sides from a higher division this season so we will have to do it again."
Report by Darren Witcoop