Former Boro marksman Carl Stewart gave Billy Miller’s men the lead six minutes from the break after looping over goalkeeper Jordan Porter.
Benny Igiehon tapped in at the start of the second half to equalise before Tom Allan controversially put the Brewers back in the lead.
The referee then took centre stage once again with ten minutes to go after awarding the visitors a dubious penalty on Dan Thirkell.
This drove Scarborough on and Cameron Murray completed the comeback with five minutes to go.
Taddy boss Miller made five changes to last week’s County Cup victory with Josh Grant, Tom Allan, Jason Mycoe, Tom Corner and Josh Greening all coming back into the starting eleven.
After a very cagey opening twenty minutes, it was the home side who had the first two efforts on goal. Both Carl Stewart and Jono Greening tried their luck from outside the penalty area but could only shoot straight at Jordan Porter in the Boro goal.
However, Scarborough unlocked the door at the other end and carved out a glorious chance as new boy Jacob Hazel drove past Josh Barrett but was denied by a terrific one v one save from Gary Stevens.
But it was Taddy who drew first blood in the 39th minute. Josh Grant’s long raking ball down the left-hand channel was met by Carl Stewart. Stewart saw that Porter had come flying off his line and the former Boro striker ever so coolly flicked over the goalkeeper.
It seemed to take an age to make its way goalwards but after bouncing once it nestled into the back of the net to give the Brewers the lead as chants of ‘he’s one of our own’ rang around the i2i stadium.
It was a bitterly cold and blustery afternoon in Tadcaster but the contest certainly heated up in the second half.
Taddy began the second half on the front foot as Dan Thirkell and Tom Corner both came close to establishing a healthier two goal cushion.
Despite that however, it was the visitors who netted next and drew level nine minutes into the second half.
A ball in behind the Brewers’ defence lead to a mix-up between goalkeeper Gary Stevens and Tom Allan which allowed Craig Nelthorpe to square to Benny Igiehon who helped himself to a tap in.
The 721 watching on football fans were being served up a Boxing Day treat as both sides were going hammer and tong.
Josh Greening must have thought he’d put his side back in front after latching onto Tom Allan’s flick on and firing low and hard only to be miraculously kept out by goalkeeper Porter.
Taddy needn’t have worried though as they did in fact retake the lead a minute later on the hour mark.
Tom Allan marked his second appearance for the club with a second goal after turning in Josh Greening’s deep free-kick.
There was certainly an air of controversy about the goal though as at first the visitors were appealing for offside before asking for handball. They may well have had a point with the latter but gesticulating with referee Tristan Greaves only resulted in a flurry of cautions.
Following the goal, the game entered somewhat of a lull as Scarborough held the majority of possession but could only waste a succession of free-kicks.
As time rapidly ticked by, Gary Stevens was on-hand to terrifically rush off his line and thwart Jacob Hazel.
However the away side were awarded a penalty kick a mere thirty seconds later. Midfielder Dan Thirkell was the guilty party after allegedly bringing down Jacob Hazel but it looked as though the Boro man was already on his way to ground.
Nevertheless the penalty kick was given and despite a touch from Stevens, Adam Bolder side-footed confidently into the top-right hand corner to set up a grandstand finale.
Taddy may have been the comeback kings in the FA Cup meeting back in August but this time it was Boro who came from behind with five minutes remaining.
After a mixture of several pinball like ricochets and Taddy not being able to clear their lines, the ball fell for tricky attacker Cameron Murray who expertly fired low into the back of the net to send the travelling fans into ecstasy.
From this moment onwards Scarborough ran the clock down effectively and held on to the victory.
Tadcaster Team: Stevens, Armstrong, Grant, Barrett, Allan, Mycoe, Stewart, Thirkell, Jono Greening (Youhill 88) ©, Corner, Josh Greening
Subs Unused: Baker, Sellars, Ibrahimi, Shepherd
Scarborough Team: Porter, Ible, Merris ©, Price, Turnbull, Humble, Hazel, Bolder, Igiehon, Murray, Nelthorpe
Subs: Bloor, Flint, Brown, Day, Morgan
Att: 721