Before the game there was an impeccably-observed minute's silence in respect of those killed, injured and affected by the atrocities in London yesterday.
Whitby made a lively start on a cold and blustery night, but a shot from skipper Dale Hopson was well off target and the game's first chance was wasted.
A couple of quick breaks from Boro came to nothing, though former Boro Academy goalkeeper Shane Bland was forced into a smart stop when dealing with a Jo Wheatley cross from close range.
When Boro made a mess of clearing a move from Whitby that looked like petering out, David Carson was left in the clear in the penalty area, though not at a good angle, and a low cross whistled through the six yard box untouched.
The clearest chance in the opening half hour fell to Boro as Bradley Fewster drew two defenders towards him and fed Junior Mondal who was left with a clear run on goal, but is finished cleared the bar as well as the goalkeeper.
The opening goal came on 36 minutes when Whitby failed to clear a left-wing free-kick, the ball fell to Niall McGoldrick who smashed home a rising drive from around seven yards.
Whitby went for a quick riposte and Aynsley Pears was forced to back pedal and tip over the bar as Michael Roberts headed from close range.
Not long after Hopson fired just over when pouncing on a poor clearance, Whitby drew level.
With 44 minutes played Pears produced a superb save to block a Michael Roberts header, but he couldn't hold on and amid flaying limbs the ball rolled over the line.
Half-time: Whitby Town 1 Middlesbrough U23s 1
It took just three minutes of the second half for Whitby to edge in front as Luke Bythway rose to meet a right-wing corner from Danny McWilliams to head in at the back post.
It was a lead that lasted just eight minutes as Boro launched second phase possession back in into the Whitby penalty area following a smart save from Bland who reacted well to a Ben Liddle free-kick. There was nothing he could do though as Tyrone O'Neill swept home through a crowded box.
Just four minutes later Boro were undone as Whitby restored their lead wen Roberts latched on to a long ball over the top. Pears saved well, but the ball rolled into the path of Luke Bythway who was left with a simple task to stroke home from close range.
Striker Bythway completed his hat-trick as Whitby gave themselves a two goal cushion on 69 minutes, rising at the back post to meet a right-wing delivery and head over Pears.
Back came Boro and Bradley Fewster worked his way into a good position on the edge of the Whitby box and curled low past Bland.
With six minutes remaining Whitby almost added a fifth, only a terrific block from Liddle kept Hopson's shot out.
They didn't need it, they'd done enough to earn a place in the final against Pickering Town.
Scorers McGoldrick 36, Roberts 44, Bythway 48, O'Neill 56, Bythway 60, 69, Fewster 72
Whitby Bland; Martin, McWilliams, May, Bullock, Bythway (Hume 82), Gell, Hopson (Capt.), Roberts (Fryett 90+1), Carson, Bell. Subs: Dixon (gk); Robinson, Caulfield.
Boro Pears; Hegarty, Cook, McGoldrick, Renton, Maloney (Wilson 83), Wheatley (Capt.), Liddle, Fewster, O'Neill (Elsdon 81), Mondal. Subs: James (gk); Reading, Torrejon.
Referee Alf Greenwood. York.