Purfleet's Jon Keeling got in behind the Aylesbury defence on more than one occasion in the first half and on 33 minutes the home side had a goal disallowed for offside.
What was to be the winning goal was scored on 40 minutes when poor defending left Paul Linger unmarked and he made no mistake in heading past the impressive Chris Day in the Aylesbury goal.
The Ducks were much more lively in the second half as both Richard Horner and Kezie Ibe (who had earlier replaced the injured Chris Bangura) forced good saves from Purfleet keeper Alex O'Reilly.
Purfleet also had chances to double their lead and in the final minute substitute Terry Bowes was denied by another superb save from Chris Day.
All in all another frustrating league outing for Aylesbury which was made even worse by Greg Williams leaving the field on a stretcher midway through the second half with a suspected back injury.