The Lions had midfielder George Cantrill dismissed in the 19th minute following a rash lunge on Alex Whittle but it was the numerically-disadvantaged visitors who took the lead eight minutes after the break when Aaron Martin headed home.
Thewlis was tripped by Guiseley keeper George Sykes-Kenworthy with 18 minutes and duly levelled from the spot.
United full-back Karl Byrne received an early booking for a foul on Dylan Barkers but Guiseley were soon reduced to 10 men when Cantrill scythed into Whittle in front of the dugouts to receive a straight red.
The Pilgrims were unable to carve out a meaningful chance until the 40th minute when Whittle forced Sykes-Kenworthy into a smart save from distance.
Guiseley took a 53rd minute when lead when Brad Nicholson’s deep corner was guided home by the head of MARTIN at the back post.
United suffered an injury blow just before the hour mark when full-backs Byrne and Whittle were both forced off.
The Pilgrims were awarded a 72nd minute penalty when Sykes-Kenworthy bundled over THEWLIS, who picked himself up to lift home another successful spot-kick.
There was a late chance for Andi Thanoj, who blasted straight at Sykes-Kenworthy, as honours ended even.
Boston (4-4-2): Peter Crook; Karl Byrne (Andi Thanoj 57), Luke Shiels, Simon Ainge, Alex Whittle (Ashley Jackson 56); Jay Rollins, Brad Abbott, Tom Platt, Jordan Thewlis; Shaun Tuton (Tom Clare 68), Dominic Knowles. Subs (not used): Nicky Walker, George Willis (gk).
Guiseley (4-2-3-1): George Sykes-Kenworthy; Reiss McNally, Scott Garner, Hamza Bencherif, Brad Nicholson; George Cantrill, Dylan Barkers; Gabriel Johnson (Aleks Starcenko 83), Aaron Martin, Aram Soleman; Kaine Felix (Sam Scrivens 77). Subs (not used): Paul Clayton, Kennedy Digie, Lloyd Allinson (gk).
Referee: Adam Williamson.
Attendance: 1,059 (55 visitors).