The Ryedale side enjoyed a hard-fought win over eight-man York RI, only winning 3-1 despite three red cards for their opponents.
Scott Preston, Jon Newton and Dean Nuttall struck for St Mary's to set up a semi-final clash with Huntington Rovers, while Liam Keenaghan replied for RI.
Huntington were taken to penalties by Church Fenton White Horse in the semi-finals of the York FA Saturday Senior Cup, but they had little trouble in overcoming the same rivals in the League Cup.
Free-scoring Chris Dyson bagged a hat-trick, with Lee Bunce, Neale Holmes and an own goal completing the Rovers’ haul.
Mikey Brown and Ollie Varley netted for division one Brooklyn as they triumphed 2-0 over premier league side St Clement's.
Grasshoppers led after only five minutes through Matthew Tiplady before Tom Metcalfe corners were nodded home by Luke Roberts and Dave Hartas.
Dale Holding then hit Hoppers' fourth shortly before the break and Dan Zambelli capped off the scoring in the second half.
Thorpe went ahead after ten minutes but Liam Robertson levelled before the interval. With no further scoring, Thorpe won the shootout 3-2.
Wigginton will face Thorpe after they defeated Riccall United 3-0. Josh Hutchinson opened the scoring for Grasshoppers with a spectacular 20-yard opener before a Tom Jackson brace.
The final will be played at Huntington Sports Club on Tuesday, May 6, kick off 6.45pm.
Riccall United finished their premier division campaign with a comfortable 6-0 victory over Terrington Glory. Gary Collier, Wayne Brook (2), Liam Olsson and Dave Heron all hit the target, with the sixth an own goal.
Selby Town and LNER Builders played out a 2-2 draw in division four.
Jordan Leybourne hit Selby’s opener before Kyle Wilkes put through his own net to level. Gary Hardcastle then gave LNER the lead before Wilkes restored parity with a last-minute penalty.
In reserve 'A', Copmanthorpe raced into a 3-0 half-time lead at Old Malton thanks to goals from Terry Hibbert, Stu Auton and Matty Pallister.
Josh Bown then struck twice for Malton but an own goal sealed the game 4-2 in Copmanthorpe’s favour.
Church Fenton White Horse defeated Haxby United 5-0.