Kab Tshimanga's 93rd minute goal was the difference as Town left Meadow Park empty handed, despite looking like picking up a point in Hertfordshire.
Tyrone Marsh had given his side the lead 14 minutes in after good work from Justin Shaibu, but Alex Bradley's long range effort six minutes before the interval ensured Town went into the break deservedly level.
A long range effort in stoppage time was blocked by Will Smith, but Wood's danger man was first to react, firing low past James Belshaw to seal the points.
Simon Weaver made four changes from last weekend's dramatic FA Trophy win as Belshaw, Warren Burrell, Josh Falkingham and Jack Muldoon all returned.
After just six minutes, Connor Hall almost opened the scoring in similar fashion to his leveller against Hartlepool, but Kane Smith was perfectly positioned to hook away the centre back's low attempt.
Despite Town's good start, Boreham Wood took the lead in the 14th minute when Justin Shaibu drove at the defence and fed Marsh, who slotted low past Belshaw.
Town searched for a response through Bradley, who fired just over from 25 yards, before Falkingham's cross was turned just past the post by Muldoon as the pressure built.
It was almost two for the hosts seven minutes before the break as the deadly Kab Tshimanga shifted the ball onto his left before crashing an unstoppable shot against the woodwork and away.
Town were back on level terms under a minute later though as Bradley produced a goal of the highest quality, bending the ball into the top left corner and in off the woodwork from a long way out, ensuring Town went into the break deservedly level.
Town began the half strongly, threatening again through Bradley whose shot flashed post Ashmore's goal.
Wood Manager Luke Garrard opted for a change in shape after the hour mark and it led to an upturn in his side's fortunes, Belshaw producing a fine save moments later to stop Keiran Murtagh heading his side back into the lead.
With the contest looking like heading for a draw, Smith's block fell to Tshimanga, who demonstrated his predatory instincts to fire past Belshaw and win the game late on.
Town: Belshaw, Falkingham, Burrell, Thomson, Kiernan (Emmett 84), Bradley, Kerry (Brown 79), Muldoon, Hall, W Smith, Hancox
Subs not used: Cracknell, Stead, Diamond
Goals: Bradley 39
Boreham Wood: Ashmore, Ilesanmi, Ricketts, Champion, Stephens, Tshimanga, Murtagh, Marsh (Mingoia 76), Fyfield (Shakes 61), Smith, Shaibu (Woodards 94)
Subs not used: Gregory, McDonnell
Goals: Marsh 14, Tshimanga 93
Referee: R Atkin
Attendance: 501 (34 away)