The hosts took the lead at Meadow Park within three minutes as Jamie Lucas turned the ball in after Clovis Kamdjo's shot was blocked.
Just before half-time Boreham Wood doubled their lead as Danny Haynes headed in Conor Clifford's cross.
Lucas sealed all three points for the home side meeting Junior Morias' cross to score his second of the afternoon.
Dover remain in the final play-off place in fifth, only ahead of Braintree on goal difference, while Boreham Wood moved a point clear of Altrincham in 21st - who have a game in hand.
Boreham Wood climbed out of the relegation places after a surprise victory over promotion-chasing Dover.