Jake Speight scored a late penalty to secure a hard-earned victory for Wrexham in the Blue Square Bet Premier.
Speight made no mistake from 12 yards after Adrian Ciezlewicz was adjudged to have been fouled by Yado Mambo.
Defender Mark Creighton had gone close for Wrexham in the first half when his header struck a post.
Both sides had chances before Speight's successful penalty secured Wrexham's second victory under Andy Morrell.
VIEWS FROM THE DRESSING ROOM
Wrexham caretaker manager Andy Morrell told BBC Radio Wales:
"They came to stop us from scoring. They defended really well. We struggled to break them down at times.
We had a lot of possession but not too many clear cut chances."
Ebbsfleet United manager Liam Daish told BBC Radio Kent:
"I've got plenty of complaints (about the penalty). I don't know what the linesman is getting involved for. The referee is on top of the situation - doesn't give it. And you've got a linesman 30 yards away - putting his flag across his chest.
"I'll have a look at the DVD - I spoke to Yado - he didn't touch him at all. There wasn't even a reaction from their players, but someone who was standing on the sidelines wanted to get involved. Maybe he was having a quiet day.
"I thought we played well. In the second half we had some great opportunities in two-against-one situations and we haven't taken advantage of them, and that's disappointing because you're not going to keep getting situations like that."