Trafalgar needed penalties to beat second division Cayton Corinthians after a 3-3 draw.
Steven Frederiksen's Cayton side led on three occasions in a thrilling cup clash, but were pegged back on every occasion, with Traf netting in the dying stages to take the game to pens.
Dave Barber spurned a couple of early openings for Cayton, while Luke Jones rattled the bar at the other end.
An own goal from keeper Chris Dove from a corner in the 35th minute handed Cayton a 1-0 lead, but an own goal from Barber then levelled matters up heading in at the break.
Back came Cayton after the interval and Tyler Beck, who had looked dangerous on the counter-attack, lobbed Dove to restore the visitor's lead.
Traf were level again 10 minutes later when Barber conceded a penalty and Danny Price swept home from the spot for 2-2.
Once again Cayton took the lead when the ball fell to Ryan Jones on the edge of the box and he found the back of the net.
But Cayton were cruelly denied a huge cup shock with just two minutes left on the clock, Mikey Barker scoring to send the game to penalties.
Player-boss Joel Ramm saw his pen saved by Luke Chambers, but Price netted his second pen of the game and Sam Pickard and Nathan Vernon also scored their spot-kicks to send Traf through, with Barber, Beck and Ste Molloy all missing their pens as Dove saved two pens.
Player-boss Joel Ramm was named as Traf's man of the match, while Frederiksen was delighted with his entire side for their efforts.
Angel Athletic were also pushed close in their semi-final clash, trailing four times before netting a late winner in a 5-4 win against West Pier.
Luke Delve was in fine form for Pier as he lashed in a hat-trick, with Matty Hillman also on the scoresheet as Pier led four occasions, with Angel being forced to battle back on every occasion.
Jackson Jowett grabbed a brace for Angel, including their last-gasp winner, with Neil Thomas, Isaac Sands and Jamie Bradshaw also finding the back of the net.
Player-boss Dan Jones singled out sub Jamie Bradshaw as his side's star man after making an impact off the bench, while Pier boss Paddy Parke singled out keeper Jordan Lee, who made a string of outstanding saves during the end-to-end cup clash.
Lee also saved two penalties during the encounter, with Martin Cooper and Sands being denied from the spot.
In Division Two, champions Angel Athletic Reserves sealed a 4-2 win against Eastfield Athletic.
Eastfield took the lead through Paul Oldroyd, but Jake McAleese levelled for Angel, cutting inside and finding the top corner.
Angel led at the break, Shaun Dolan tapping in for 2-1.
Jake Moore's effort extended Angel's lead to 3-1 after the interval, but skipper Jamie Hartley scored for Eastfield to give them hope.
Angel weren't to be denied though and Kieron Glave found the back of the net with his first touch after coming off the bench to wrap up a 4-2 win for Macauley Riley's side.
Dom Barber was Angel's man of the match, while keeper Jordan Wood stood out for Eastfield.
Elsewhere, Castle Tavern and Roscoes Bar drew 4-4.
In an end-to-end clash Roscoes opened up a 2-0 lead as Sam Colling netted twice, but Tavern battled back superbly to take a 3-2 lead, Paul Mills hitting two and Darren Lang also scoring.
Roscoes hit back again as Colling sealed his hat-trick and Graeme Farrah got his name on the scoresheet, but sub Nathan Spencer's goal sealed a share of the spoils for Wayne Shaw's Tavern side.
Chris Rooke was Tavern's star man, while hat-trick hero Colling stood out for Bar.
SCARBOROUGH FA SUNDAY CUP SEMI-FINALS
Trafalgar 3-3 Cayton Corinthians (Traf won 3-0 on pens), West Pier 4-5 Angel Athletic.
Angel Athletic Reserves 4-2 Eastfield Athletic, Castle Tavern 4-4 Roscoes Bar.