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Dover slipped to their seventh home National League defeat of the season after a disappointing display at Crabble on Saturday.
A 32nd minute penalty from Sorba Thomas was all that separated the sides at the break, but that was only half the story as Whites failed to register a shot on target until the 42nd minute.
A terrible mistake by Scott Doe gifted Wood their second, scored by Justin Shaibu just before the hour, after which there was no way back for Andy Hessenthaler's side.
One small positive for Whites was the return of skipper Kevin Lokko back in the side for the first time since October 26.
He and Josh Passley were both fit again after ankle and hamstring problems respectively with Jack Munns and Will De Havilland the men dropping to the bench.
With 10-goal top scorer Inih Effiong still ruled out by a knee injury Whites again went with Ricky Modeste and Steven Rigg up front.
Rigg had an early half-chance when Jai Reason's free kick was headed down to him by Lokko but stretching, the Whites striker was only able to lift his shot over.
Michael Woods broke into the box on 18 minutes but was unable to get his shot away before being dispossessed but chances were otherwise scarce.
Passley and Bobby-Joe Taylor got forward well on occasions, but there was no cutting edge.
Kabongo Tshimanga was Boreham Wood's dangerman and the visiting No.9 gave a glimpse of his ability on 21 minutes when he took one touch to control a cross from Thomas and then saw his rising shot clip the top of the crossbar.
The visitors continually looked threatening on the break and it was following another swift counter that they went ahead from the spot.
Kurtis Cumberbatch was adjudged to have caught Kane Smith in the box and Thomas scored in the bottom corner, sending Lee Worgan the wrong way from the spot.
Cumberbatch was also booked for the challenge and he was joined into the book shortly after by Reason following another foul.
Dover's first shot on target did not arrive until three minutes before half-time when Rigg fired straight at Wood keeper Nathan Ashmore after Paul Rooney had picked him out following a surging run.
Moments later the striker became the third Whites man to go into referee Adrian Quelch's book, for dissent.
Boss Hessenthaler made a change at half-time replacing Cumberbatch with winger Anthony Jeffrey.
He also changed formation, switching to a back four with Rooney pushing into midfield.
Jeffrey was quickly involved combining with Taylor to create a chance for Woods who failed to connect cleanly with his shot.
Wood's Tyrone Marsh then almost caught Worgan out with an early shot which had the Whites keeper scrambling across goal before the ball went wide.
Whites were still in the game at that stage but with the clock approaching the hour mark a disastrous defensive error enabled Wood to double the lead.
Centre-half Scott Doe was robbed by Tshimanga as he attempted to shepherd the ball out for a goal kick and the Boreham Wood man then squared the ball for Shailbu who won't have an easier finish.
Another defensive slip, this time by Rooney, almost let in Marsh but Worgan was able to block with his legs.
Rooney's afternoon continued with a booking, and as Wood continued to exert their dominance, Tshimanga should have made it 3-0 after breaking clear but Worgan did well to save with his feet.
Dover remain on just two home wins for the season, while Boreham Wood's win stretched their unbeaten run to seven games.
Dover: Worgan, Passley, Taylor, Doe, Lokko, Rooney, Woods, Cumberbatch (Jeffrey 46mins) Reason (L'Ghoul 63mins), Modeste, Rigg (Ratti 76mins); Subs: De Havilland, Munns.
Boreham Wood: Ashmore, Ilesanmi, Ricketts, Champion, Stephens, Murtagh, Tshimanga, Marsh, Thomas, Smith, Shaibu (Shakes 62mins); Subs: Woodards, Mingola, McDonnell, Fyfield.
Attendance: 728
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