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Stevenage 1 Ebbsfleet 0
Ebbsfleet face already-relegated Lewes at Stonebridge Road on Monday still with work to do in order to confirm their own Blue Square Premier League status next season.
Kezi Ibe, back from a loan spell with Conference South leaders AFC Wimbledon was on the bench at Broadhall Way, with manager Liam Daish without as many as 10 of his first team players with his injury-hit squad facing three more games in the next week.
They travel to fifth-placed Histon on Thursday, and struggling Weymouth, who have slipped into the bottom four, on Saturday.
Borough, who shattered FA Trophy holders Fleet's dreams of a lucrative return to Wembley last month, maintained their chase for the play-offs thanks to Mitchell Cole's 32nd-minute winner. He raced half the length of the pitch, before firing past Lance Cronin.
Callum Willock earlier hit the post, and had another effort saved by Cronin, who also kept out Gary Mills' header. Fleet defender Leon Crooks was denied by a reaction save from Borough keeper Chris Day.
Sacha Opinel was booked for a heavy challenge on Lawrie Wilson, and later withdrawn by Daish, while Trophy semi-final winner Peter Vincenti missed a great chance to score a second before the end.