The Pilgrims' progress came thanks to a brace from the exceptional Andy Kirk, who had also scored twice in the reverse fixture earlier in the season.
As usual Wycombe fell behind as they have done so often in games this season. On this occasion it took only four minutes for the visitors to take the lead.
Kirk, having been denied just a few seconds earlier by a brilliant save by Frank Talia didn't waste the second gilt-edged chance to come his way as he fired past the Aussie.
The home side wasted a glorious chance on the half-hour, Nathan Tyson got free down the left and the on-rushing Steve Claridge met his cross, but the former Leicester hitman somehow steered his effort wide.
The home side though were back on terms nine minutes later as Tyson latched on to a through ball from Keith Ryan, was flattened by Nathan Abbey for which the keeper was booked. Jonny Dixon, making his first start since returning from a loan spell at Aldershot, dispatched the spot-kick with ease.
Boston started the second period strongly, Kirk smashing over from 20 yards as the Northern Ireland International hunted his second of the game on 50 minutes.
Six minutes later Claridge missed he target again while in the six-yard box as he headed Steve Guppy's free-kick over the bar. Wycombe's wing wizard Guppy combined with Claridge on 67 minutes with a neat one-two, but the one-time England winger's shot was into the sidenetting.
Boston always looked dangerous on the break; Kirk took advantage of a defensive mistake by Gary Silk on 75 minutes, but wasted the chance shooting over the bar.
As if to prove they were still very much alive, Boston struck the post with a towering header by Jason Lee from an inch-perfect Steve Boyack cross on 80 minutes.
The pressure from the visitors told on 85 minutes with Lee heading into the path of Kirk who finished with aplomb past the exposed Talia to restore the Pilgrims' lead.
Despite six minutes of injury time, the visitors held firm to record a useful victory.