The Seadogs came into their marathon trip south on the back of five unbeaten games and clean sheets.
Boro did apply some early pressure with Harry Green's free-kick curling inches the wrong side of the post and a thunderous strike from Alex Brown from distance tipped around the post by the Saints' keeper Maxted.
Scarborough created further opportunities with the impressive Luca Colville going close and Harry Green seeing another shot saved.
However, against the run of play, the hosts took the lead two minutes into first half stoppage time from a corner.
Boro boss Jono Greening said the timing was gut-wrenching:
"It's criminal when you concede a goal with 30 seconds left before half time. We were in control, there was nothing in the game and we just switched off".
There was then a lengthy delay early in the second half when Scarborough's Alex Purver collided with the referee, the latter receiving treatment from the medical team from both sides.
The 2nd half saw fewer chances for Boro, who ended up bringing on all 5 subs.
The Seadogs pushed for a late leveller but were caught out by a 94th second goal for the home side.
A mix-up from a Lewis Maloney header back to keeper Ryan Whitley saw Brackley's sub Miracle Okafor place the ball into the empty net.

Over 70 seadogs fans made the 400-mile round trip south.

Boro boss Jono Greening spoke to Paddy at full-time:
The Seadogs entertain Merseysiders Marine next Saturday with a 3pm kick-off.


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