Wafula's eighth minute header handed the Pilgrims the lead against the Red Imps at The Jakemans Stadium but the visitors soon levelled through Bruno Andrade.
Second half goals from Shay McCarten, Harry Anderson and a second for Andrade wrapped up Lincoln's victory.
Boston (4-4-2): George Willis; Ben Middleton (Sam Topliss 64), Ryan Qualter, John McCombe (Trialist J 55), Ashley Jackson (Jordan Gough 71); Jonathan Wafula (Nicky Walker 75), Brad Abbott (Spencer Harris 64), Andi Thanoj, Nathan Arnold; Jonny Margetts (Andre Johnson 75), Adam Marriott (Grant Roberts 77). Sub (not used): Dylan Parkin.
Referee: Darren Drysdale.
Attendance: 1,119 (464 visitors).