Clayton Donaldson's third goal in two games ensured Crewe reached the FA Cup second round despite them being pushed all the way by non league Ebbsfleet.
FA Trophy holders Ebbsfleet dominated from the off with Neil Barrett almost giving them a dream start when his overhead kick flew wide of the post.
Mark Ricketts then nearly caught Steve Collis off his line with a free-kick, while Kezie Ibe forced a good save.
But Donaldson snatched the crucial goal with a smart turn-and-shot.
Crewe: Collis, Brayford, O'Donnell, Baudet, Jones, Miller (Zola 46), O'Connor, Bailey, Grant (Carrington 46), Moore, Donaldson.
Subs Not Used: Woodards, Tomlinson, Murphy, Pope, Elding.
Booked: O'Donnell, Grant.
Goals: Donaldson 34.
Ebbsfleet United: Cronin, Ricketts, Smith, Charles, Opinel, Hand (Long 80), Barrett, Stone, Purcell, Ibe (Shakes 62), Gash.
Subs Not Used: Hawkins, Slatter, Pooley, Mott, Bowes.
Booked: Hand, Ricketts, Charles.
Att: 2,593
Ref: Richard West (E Yorkshire).
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