Calum Willock's last-minute header gave Ebbsfleet their first win of the season after twice coming back from behind.
Jai Reason put Braintree ahead from the spot as Clint Easton fouled Sean Marks.
Adam Bailey-Dennis then brought down Willock in the area with Tom Phipp converting from the spot, before Reason slotted home Ben Wright's cross.
Scott Ginty equalised from the spot with five minutes left after a Matt Paine foul before Willock's last gasp header gave Fleet the win.
VIEWS FROM THE DRESSING ROOM
Ebbsfleet manager Liam Daish told BBC Radio Kent:
"The lads showed a bit of character in coming back from two goals down. In the end, we pinched the winnner but they're a good strong tough team.
"[On his sending off] I've tried to make a sub and the assistant put the wrong number up. I questioned it and he sent me off, which is a bit strong.
"There is still a bit of work to be done but this will give the lads the confidence to get it done."
Braintree Town: McDonald, Peters, Paine, Bailey-Dennis, Thomas, Yiadom (James-Lewis 84), Symons (O'Connor 70), Davis, Reason, Marks, Wright (Chilaka 76). Subs Not Used: Ashlee Jones, Quinton.
Booked: Davis, Paine, Thomas, Reason, Bailey-Dennis, O'Connor.
Goals: Reason 15 pen, 69.
Ebbsfleet United: Edwards, Stone, Simpemba, Easton, Herd, Enver-Marum, Howe (Azeez 74), Marwa, Phipp, Willock, Shakes (Ginty 81). Subs Not Used: Welch, Fakinos, Stavrinou.
Goals: Phipp 61 pen, Ginty 87 pen, Willock 90.
Ref: Steve Bratt (W Midlands).