The lively Jack South opened the scoring for Andy Thorpe's reserve team in the sixth minute, but within nine minutes Ash Townley had levelled for the first team.
South once again broke free of the Scalby 1sts defence before half-time to restore the lead for the reserves.
A Si Rigg own goal doubled the lead for the Reserve League side, and although Rob Speight pulled another goal back for the first team seven minutes from time it came too late to save Sam Medd's troops.
Thorpe said: "All the lads were outstanding today, Brandon Catherall was the clear man of the match for us as he was excellent in defence, with South also playing very well."It was a great game and it was good to secure the bragging rights at the club with this success."
Edgehill Reserves lost out 5-4 on penalties to West Pier Reserves after being held 1-1 at home after extra-time.
Benny Davis put the home side in front before the interval, then Dave Wedge's pass released Rich Tolliday, who slotted in the second-half leveller.
Nathan Barber was then dismissed for Edgehill but here were no further goals in normal time.
The game then went to extra-time, Josh Wallace, on making his comeback from a lengthy spell out through injury, had to go off leaving the hosts with only nine men.
There was no further score so the tie went to penalties, and a save from Pier keeper Richard Curtis proved vital as they won the shootout 5-4.
The scorers of the spot-kicks for Pier were Gavin McGough, Ryan Goodworth, Tolliday, Konrad Sygitowcz and Mikey Anderson, who netted the winning penalty. Jason Prosser had an impressive match in midfield for Johnny McGough's team.
Edgehill's man of the match Carl Hepples, Aidan Thurston, Josh Fergus and Robbie Scarborough notched from the spot for Edgehill.
Filey Town Reserves came back from a goal down to claim a 5-1 success at Ayton Reserves.
Richard Howes marked his Ayton debut with an opening goal after only two minutes, smashing in a 25-yard strike into the top corner.
Town levelled on 20 minutes through Billy Coyne after a goalmouth scramble despite Ayton's protests that a foul had been committed by the visitors during the melee.
On the stroke of half-time, 16-year-old Harry Keary scored a superb goal after a powerful run to put Town in front.
The visitors increased their lead 10 minutes into the second half when Tommy Wilson, forced to play up front rather than his usual central midfield role, scoring from outside the area after the home defence had switched off.
Coyne's tap-in after some fine build-up effectively booked Filey's spot in the next round, Howes and Town sub Tom Orange both saw red shortly afterwards as tempers frayed, then Max Gage's header in the final minute rounded off the scoring.
Town boss Dan Kempson said: "We had six or seven players missing so the lads did really well today. Tommy Wilson played out of position up front but put a great shift in and had a lot of chances, he was our man of the match, while Lee Lambert also did well in the centre of midfield.
"It was good to see the lads come back from a bad loss last weekend and get a win today, especially with so many enforced changes."
Ayton chief Steven Frederiksen said: "Nicko Dunn was our man of the match in central midfield, while Nathan Sutherland also did well on the left of midfield. We were well and truly in the game in the first half, but switched off after the half-time break.
"We had to make a lot of changes for this game due to injuries, the age-gap between our two full-backs was 35 years, with Paul Tymon on the left with 16-year-old Mikey Sharp on the right."
Itis Itis Rovers cruised to an 8-0 home win against Commercial.
Sean Bloom's strike put Rovers 1-0 up at the break, then player-boss Mikey Barker came on at half-time and scored the next three games to secure the win for the hosts.
Further goals from Callum Myers (2), Sam Pickard and Ryan Matson wrapped up the win, with Pickard's a great strike from the edge of the penalty area and Matson shimmying past a Commercial defender before sweeping the ball past the keeper.
Curtis Rose was man of the match for Rovers again, this time with a fine display from central midfield.
Cayton Corinthians also moved into the next round with a 5-1 home triumph against Goldsborough United.
Michal Szalabski opened the scoring for Cayton, Jake McAleese adding a second with a free-kick before Daniel Booth smashed a 25-yarder into the top corner to make it 3-0 at the interval.
United hit back after the break, but a penalty from Cayton midfielder James Barber, who was their man of the match, and a Jake Sands strike after he had followed up a shot from Luke Foster saved by the United keeper, made sure of the win for the hosts.