John Akinde's injury-time winner for Ebbsfleet ensured Stafford remain 10 points adrift of safety. The hosts almost took a first-half lead when striker Nathan Smith was denied by the feet of Fleet keeper Lance Cronin.
Stafford continued to apply pressure but strikes by David McNiven and Samy Mawene efforts were both kept out.
The game looked to be heading for a draw until Akinde slotted home Luke Moore's pass from the left just seconds before the final whistle.
Stafford: Alcock, Sutton, Daniel, Arnolin (Olaoye 86), Richards, Street, Draper, Mawene, Grayson, Smith (Hamilton 55), McNiven.
Subs Not Used: Allen, Ingram, Hopkinson.
Ebbsfleet: Cronin, Ricketts, Hawkins, Smith, Opinel, Bostwick, Akinde, Barrett, Long, Moore, McPhee.
Subs Not Used: French, Nade, Coleman, Stubbs, Purcell.
Booked: Akinde.
Goals: Akinde 90.
Att: 653
Ref: D Mohareb (Cheshire).
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