Knowles' well-taken first half brace, scored in the 37th and 43rd minutes, accounted for Kidderminster Harriers at The Jakemans Stadium.
Jordan Thewlis and debutant Frank Mulhern were involved in the build-up to both Knowles goals as United ended a perfect week with nine points from nine.
Mulhern was included as one of four United attackers in a bold selection by United boss Craig Elliott following his loan arrival from Stockport County on Friday.
Peter Crook kept out an Austin Samuels header in the opening stages before opposite number Will Mannion made two fine saves to deny Mulhern and Andi Thanoj in quick succession.
Harriers continued to pose a threat on the break and Ashley Chambers saw an effort deflect and clip the outside of the post while Crook blocked bravely and decisively at Samuels’ feet.
United took the lead eight minutes before half-time when Jay Rollins and Thewlis combined to tee up Mulhern and he chipped back across goal for KNOWLES to head home from close-range.
The Pilgrims doubled their lead six minutes later when Thewlis and Mulhern combined once more for KNOWLES to sail home a low effort from 18 yards which took the slightest of deflections on its way in.
The second half was a quiet affair, with Crook making one particular save of note to deny Samuels at full stretch.
United maintained their two-goal lead with relative ease to stretch the gap between themselves in fifth and the rest of the play-off pack.
Boston (4-2-3-1): Peter Crook; Alex Penny, Luke Shiels, Simon Ainge, Alex Whittle; Andi Thanoj, Tom Platt; Jay Rollins, Jordan Thewlis (Ashley Jackson 87), Frank Mulhern (Shaun Tuton 88); Dominic Knowles (Jonathan Wafula 79). Subs (not used): Scott Garner, Martyn Woolford.
Kidderminster (3-4-2-1): Will Mannion; Cliff Mayo, Keith Lowe, Ryan Johnson; Sam Austin, Milan Butterfield (Ed Williams 89), Alex Prosser, Ollie Shenton (Samir Nabi 73); Ashley Hemmings, Ashley Chambers; Austin Samuels. Subs (not used): Ethan Freemantle, Correy Davidson, Tom Palmer (gk).
Referee: Ed Duckworth.
Attendance: 1,278 (79 visitors).