Thewlis' 50th minute penalty separated the sides at The Jakemans Stadium but he was one of four players sent off in a frantic finale.
Thewlis and Jay Rollins saw red, alongside Leamington's Junior English and Jordan Murphy, as referee Dean Watson handed out the punishments following a heated melee following English's foul on Rollins.
Ahead of kick-off, United boss Craig Elliott had handed league debuts to full-back Karl Byrne and striker Dominic Knowles and both players responded with positive performances.
The best saves of the opening stages were made by Peter Crook in the United goal following a Murphy drive from 20 yards and a Kaiman Anderson effort from a similar distance.
United gradually asserted themselves and visiting keeper Jake Weaver had to make a save with his legs to deny Simon Ainge following a partially-cleared corner.
Brad Abbott nestled an effort a fraction wide while Rollins bundled the ball wide of the near post after Knowles had helped on Thewlis’ low cross.
Knowles went even closer just 19 seconds after the restart, with Weaver again using his legs to good effect.
United took the lead on 50 minutes when English was adjudged to have fouled THEWLIS and the same player picked himself to lift home the resulting spot-kick high to Weaver’s left.
Thewlis went sprawling in the box again moments later but referee Watson was unmoved on the second occasion.
Weaver made two further saves to deny Thewlis, with Knowles’ 20-yarder being deflected wide too and substitute Shaun Tuton firing two efforts off target when well-placed.
Carnage descended following English’s hack at Rollins. Both players were eventually dismissed for squaring up to each other and Thewlis and Murphy followed for their respective parts in proceedings.
United duly saw out seven minutes of additional time to record their first win of the campaign and extend their unbeaten start in the process.
Boston (4-4-2): Peter Crook; Karl Byrne, Luke Shiels, Simon Ainge, Alex Whittle; Jay Rollins, Brad Abbott (Ashley Jackson 90), Tom Platt, Jordan Thewlis; Jake Wright (Shaun Tuton 74), Dominic Knowles (Andi Thanoj 90). Subs (not used): Tom Clare, George Willis (gk).
Leamington (4-2-3-1): Jake Weaver; Junior English, Jamie Hood, James Mace, Jack Lane; Joe Clarke, Callum Gittings (Reece King 73); Jordan Murphy, Jack Edwards, Kaiman Anderson (Connor Taylor 90); Josh March (Ravi Shamsi 73). Subs (not used): Gift Mussa, Kieran Dunbar.
Referee: Dean Watson.
Attendance: 1,083 (27 visitors).