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Bradley Bubb's first-half goal proved decisive as Ebbsfleet took the honours at Stonebridge Road on New Year's Day.
Dartford won 2-1 when the two sides met on Boxing Day but Fleet gained revenage in National League South.
It was another competitive game with the two teams evenly matched - and both on course for the play-offs.
While Dartford named an unchanged side following their 2-1 Boxing Day win at Princes Park, Daryl McMahon made four changes.
Out went Jack Connors, Marvin McCoy, Darren McQueen and Stuart Lewis with Sean Shields, Mark Phillips, Bubb and Jack Powell in.
Fleet should have taken the lead on 17 minutes. Powell took a quick free-kick to find Andy Drury and his early cross looked perfect for Bubb. But the Fleet forward somehow fluffed his lines, and keeper Deren Ibrahim was able to scramble across and make a save.
Dartford had settled much the better, however, and they soon started to create opening of their own, albeit none as clear-cut as Bubb's.
Indeed, Keaton Wood's long-range effort was far from a shot as keeper Nathan Ashmore had to be alert to turn the ball over the bar.
Tom Gardiner then hooked his shot wide and Ashmore was out smartly to clear a cross with Duane Ofori-Acheampong closing in.
Fleet had three players booked in the first half as referee Alan Dale put his authority on the game.
The home side went ahead four minutes before half-time when Powell danced into the penalty area and took his time before squaring for Bubb, who again couldn't miss in front of goal - and this time he didn't.
Danny Harris was in behind the Fleet defence just before half-time but his shot lacked any power while Luke Wanadio fired a free-kick into the wall.
Chances were at a premium after the break although Kedwell blazed over when left unmarked from a Powell corner.
Darts introduced Tom Murphy for his debut just after the hour but he struggled to have an impact on the game.
Darts had four upfront by the time Ryan Hayes came off the bench but they were unable to fashion a clear sight of Ashmore's goal.
Ebbsfleet: Ashmore, Cook, Shields (McCoy 69mins), Phillips, Winfield, Clark, Rance, Drury, Kedwell, Bubb (McQueen 76mins), Powell. Subs not used: Miles, Lewis, Deering.
Dartford: Ibrahim, Gardiner (Pugh 63mins), Wood, Bonner, Vint, A Brown (Hayes 79mins), Noble, Bradbrook, Ofori-Acheampong, Harris, Wanadio (Murphy 63mins). Subs not used: Dembele, Coxall.
Attendance: 2,564.