Jayden Stockley's late winner handed Woking the three points and kept Ebbsfleet firmly planted in the Blue Square Bet Premier relegation zone.
Kevin Betsy had squandered an early penalty for Woking, shooting wide after Paul Lorraines fouled Loick Pires.
Home keeper Aaron Howe saved from Ashley Carew before Woking saw Billy Knott's effort ruled out for offside.
But the Surrey side struck in the 89th minute when Bradley Bubb's centre cannoned off Stockley and into the net.
Ebbsfleet, who have now gone eight games without a win and are four points adrift of safety, were dealt a further blow after the final whistle when Carew was sent off after a confrontation with Betsy.
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Woking manager Garry Hill told BBC Surrey:
"We knew with the heavy pitch we had to go away from our usual football way and try and stop them a little bit more from winning those second or third balls.
"We got the ideal start with the penalty but it hasn't hit the target and it happens. I felt the first half was quite even and I thought in the second half the longer the game went on we fancied ourselves.
"We created the better chances and I know it's a late goal but it's a big three points and we got our reward late on."