Ebbsfleet, who needed a win to keep the pressure on table toppers Maidenhead United, flew out of the traps and grabbed a foothold with the first chance of the game.
Sean Shields and Jack Connors found space down the left, with the latter crossing to the near post where Bubb flicked an effort past recalled goalkeeper Valery Pajetat.
That goal didn’t deter Margate, as Chris Sessegnon found some room down the left flank, flashing a cross just wide of the far upright.
Sam Deering had a couple of chances to extend his team’s lead but hit one shot well wide, while the other flew down Pajetat’s throat from 20 yards.
Although Ebbsfleet enjoyed the lion share of possession in the first half that’s as close as they got to scoring their second as Margate controlled the game in the second period.
That said, chances were still limited as Nathan Ashmore was largely untroubled in the Ebbsfleet goal.
The closest the Blues came to scoring was just after the hour mark when Stephane Ngamvoulou nodded towards goal following Michael Thalassitis’ header across the box, only to see his effort cleared off the line.
Dave Martin struck a couple of efforts over the bar, with Jack Evans’ free-kick and Thalassitis’ fierce effort finding a similar destination, as Margate failed to upset their opponents with a late goal.
Margate: Pajetat, Hamilton, Sessegnon, Rogers, Moore-Azille, Swift, Ngamvoulou (McFarlane 90), Evans, Thalassitis, Morgan (Akindayini 17), Martin. Subs not used: Palmer, Kallmeier, Cumbers.
Man of the Match: James Rogers