Simon Weaver gave the number nine shirt to loan signing from Grimsby Town, Dayle Southwell, who produced an excellent performance.
Southwell made an early impression with a low centre from the right, before he gathered Chris Hall’s flick on and forced Ashley Timms into a close range save.
Boston began to hit their stride and captain, Scott Garner pushed forward to head, Rene Steer’s free kick over the bar.
Town fell behind after eleven minutes when Ricky Miller’s low cross from the left was glanced into the far corner by Marc Newsham.
Ex Townie, Peter Bone, tested Craig MacGillivray from 25 yards as Boston stepped up the pressure, and they increased their lead on 23 minutes.
Leigh Franks brought down Jake Hall in the penalty area and Newsham gave MacGillivray no chance from the spot.
Things got even worse for Town five minutes later when the unmarked, Spencer Weir-Daley, fired Miller’s cross into the far corner to make it three.
Town, generalled by Adam Bolder, began to fight back.
A deep Merris centre found Franks, but his shot was cleared off the line and a Michael Woods drive was deflected for a corner.
The half ended with Timms making a fine block from Bolder to prevent Town reducing the arrears.
At the break, Craig Nelthorpe, Dominic Rowe and Liam Hardy replaced Bolder, Anton Brown and Woods, as Town made all three substitutions.
This gave Harrogate a new lease of life and Southwell sent Hardy down the right, but Boston scrambled away his searching cross.
Undeterred, Hardy tried his luck on the left, but his low centre across the goal found no takers.
However, on 68 minutes, Town finally got on to the scoresheet.
Boston’s, Indy Aujla, was booked for a foul and Merris’s free kick was rifled home by Hardy as Boston failed to clear their lines.
The Pilgrims retaliated quickly and Miller’s cross shot flashed narrowly wide of the far post.
But Town were not to be denied and Southwell headed another Merris free kick just wide of the upright.
With 20 minutes left. Dominic Rowe’s speculative 30 yard lofted drive deceived Timms and made it 3-2.
As the game entered the final five minutes,Liam Hardy was flattened inside the area by Boston sub Netan Sansara, and Referee Neil Hair had no hesitation in brandishing a red card.
Southwell crowned a fine debut when he sent Timms the wrong way with the resulting penalty to earn Town an unlikely point.
Town, 1 MacGillivray, 2 Samuels,3 Merris, 4 Bolder (Nelthorpe 45 mins), 5 Franks, 6 Killock (c),
7 Nowakowski, 8 Brown (Rowe 45),9 Southwell, 10 Woods (Hardy 45), 11 Hall.
Unused subs, 15 Taylor, 16 Worsfold.
Scorers Hardy 68,Rowe 71, Southwell 85 pen.
Att 921 ( 37 away).