Wafula stooped to head home Ashley Hemmings' pinpoint delivery from the left as the Pilgrims snatched all three points against their 10-man visitors.
Dan Bradley's header had put Harriers ahead, only for Jordan Keane and Ben Middleton to turn the tables in United's favour before half-time but substitute George Waring levelled moments after Lee Vaughan had been red-carded for a rash challenge on Hemmings.
The pulsating encounter, with George Willis preferred to Jon Stewart in the United goal, got under way with Jake Beesley seizing on a loose Vaughan pass to motor goalwards, only for Declan Weeks to get back with a fine covering challenge.
The Pilgrims fell behind with 15 minutes played when BRADLEY steered home Weeks’ corner with United appealing in vain for a foul on recalled keeper Willis.
Visiting stopper Brandon Hall excelled to keep out a goalbound Reece Thompson drive before United levlled with 24 minutes on the clock as KEANE got up to glance home Hemmings’ inswinging free-kick.
Hemmings teed up Stephen Brogan to fire off target before providing the ammunition for United to edge ahead on the half-hour mark when MIDDLETON eventully forced the ball over the line following an almighty scramble in the Kidderminster box.
Bradley poked an effort wide on the stroke of half-time but the Pilgrims warranted their interval advantage and came close to extending it through Hemmings and then Beesley at the start of the second period.
Ryan Qualter whistled an effort wide following a James Clifton assist before Kidderminster were reduced to 10 men at the three quarter mark of the match when Vaughan was dismissed for a reckless challenge on a marauding Hemmings.
Harriers made a mockery of their numerical disadvantage by levelling five minutes later when WARING struck at the back post after Willis had excelled to keep out Ryan Croasdale’s drive.
Hall made a fine stop to thwart Thompson and with the match seemingly meandering towards stalemate, Hemmings stepped up to produce a mazy run and fabulous cross from the left which was powered home by the head of WAFULA at the back post.
Boston (4-4-2): George Willis; Ben Middleton, Ryan Qualter, Jordan Keane, Stephen Brogan; James Clifton (Jonathan Wafula 83), Brad Abbott, Andi Thanoj, Ashley Hemmings; Reece Thompson, Jake Beesley (Kabongo Tshimanga 76). Subs (not used): Jamie McGuire, Taron Hare, Gregg Smith.
Kidderminster (4-3-3): Brandon Hall; Lee Vaughan, James Pearson, Fraser Horsfall, Sam Austin; James McQuilkin, Declan Weeks, Ryan Croasdale; Emmanuel Sonupe (George Waring 69), Joe Ironside, Dan Bradley. Subs (not used): Andre Brown, Elton Ngwatala, Kennedy Digie, Nathan Vaughan (gk).
Referee: Anthony Tankard.
Attendance: 1,158 (101 visitors).