Dagenham opened the scoring after 25 minutes when Sam Ling curled one in from inside the area.
The hosts were on level terms just six minutes later when Ashley Nathaniel-George let fly from range and left Elliot Justham stranded in the Daggers goal.
Maidenhead completed the first-half turnaround three minutes later after Reece Smith forced Justham into a save, and Emile Acquah was on hand to tap in the rebound.
The visitors went in search of an equaliser and almost had one but Ling failed to find the target with a good chance.
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