A Jefferson Louis brace helped Wrexham recover from Neil Barrett's early goal.
Barrett headed in Stacy Long's corner, before Louis got on the end of Tom Kearney's right-wing cross to tap in.
After the break, Louis powered in a header from Shaun Whalley's cross, before Darius Charles fouled Simon Brown to concede a penalty.
Brown stepped up to hammer home from the spot, Michael Gash's injury time tap in from Mark Ricketts' cross only serving as a consolation.
The victory ended a two-game losing streak for the Dragons, and finished Ebbsfleet's six game unbeaten run.
Wrexham boss Brian Little:
"We were always going to be a little bit nervous in this game so our plan was to be a little bit longer and turn them to try to put them under pressure and try to concentrate on not going a goal behind.
"Then we did, so we were under pressure again, but I thought the commitment and desire to get something out of the game was great.
"We're trying out best. We made a couple of mistakes. At 3-1 we'd made the game comfortable, then switched off for 10 seconds and that got them back into it.
"I was pleased when the final whistle went."
Wrexham: Ward, Spender, Steve Evans, Kempson, Tremarco, Simon Brown, Kearney, Mackin (Baynes 75), Taylor (Proctor 46), Louis (Smith 75), Whalley.
Subs Not Used: Anthony Williams, Mike Williams.
Booked: Kearney, Louis.
Goals: Louis 37, 51, Simon Brown 77 pen.
Ebbsfleet United: Cronin, Ricketts, Smith, Charles, Opinel (Slatter 81), Long, Hand, Barrett, Shakes (Ibe 55), Gash, Moore.
Subs Not Used: Stone, Pooley, Mott.
Booked: Hand, Smith, Charles.
Goals: Barrett 27, Gash 90.
Att: 3,132
Ref: S Rushton (Lancashire).
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