Matt Bloomfield sealed victory for Wycombe deep into stoppage time in a match marred by red cards and Boston's manager being sent from the dugout.
Boston boss Steve Evans was removed 55 minutes in following an altercation with Wycombe's Tommy Doherty.
Three minutes later Doherty saw red for stamping out at David Galbraith.
Then 60 minutes in, Drewe Broughton was sent off for a second bookable offence and it was left to Bloomfield to settle the affair with a curling free-kick.
Boston Utd: Marriott, Rusk (Richie Ryan 56), Albrighton, Ellender, Tim Ryan, N'Guessan, Greaves, Galbraith, Farrell, Broughton, Green (Cotton 42), Cotton (Maylett 72).
Subs Not Used: Elding, Holland.
Sent Off: Broughton (60).
Booked: Broughton, Albrighton, Farrell, Greaves.
Wycombe: Batista, Stockley, Antwi, Williamson, Golbourne, Betsy, Doherty, Grant (Martin 82), Bloomfield, Easter (Stonebridge 90), Mooney.
Subs Not Used: Young, Palmer, O'Halloran.
Sent Off: Doherty (59).
Goals: Bloomfield 90.
Ref: A Taylor (Manchester).