The hosts, who have had only three home wins this season, had high hopes of building on their surprise 3-0 win at Morecambe earlier in the week, but were frequently outplayed by the stylish Dagenham side, despite them being hit by injuries this week.
Daggers manager John Still said "We deserved to win - we could have another three goals in the second half despite Scarborough pushing everything up front in the late stages."
From the outset Dagenham looked the more determined side and almost went ahead after two minutes through Shane Blackett who fired wide, while man-of-the-match
Scott Griffiths masterminded a great move with Glen Southern but the latter stumbled as he attempted to shoot on goal.
Scarborough had their chances with Steve Baker having a chance headed off the line and Neil Bishop went close with a speculative shot which former Welsh international goalkeeper Tony Roberts did well to save.
But poor finishing and a lack of players up front repeatedly saw opportunities lost, with the best example being when Tony Hackworth put the ball across the open goalmouth from the left only to find no-one around to finish off the move.
Dagenham continued to have the upper hand towards the break thanks to Craig Mackail-Smith and Southern who forced Scarborough keeper Leigh Walker to
make two fine saves.
Chris Hughes tried hard to score in a goalmouth melee after Roberts dropped the ball and then seconds later had another chance which he squandered.
The visitors tightened their grip on the run of play in the second half and almost broke the deadlock when Mackail-Smith tested Walker who made an applause-earning diving save.
It came as no surprise when Dagenham eventually found the net after 70 minutes thanks to Griffiths, who played a neat one-two with Chris Moore, before blasting the only goal of the game into the back of the net.
Scarborough rallied in the closing stages, and should have produced an equaliser through David McNiven, who created a fine chance but again there was no-one in the goalmouth to crack the ball into the net.
Hackworth produced two further chances, but Dagenham proved to be as strong in defence as in attack.