The hosts took an early lead, when with just six minutes on the clock Romaric Logon's well-placed shot from outside the penalty area found the the bottom corner. Waltham Abbey doubled the lead on 18 minutes, when Spencer Harris headed in.
The Hawks pulled a goal back courtesy of an Ibrahima Sonko long-throw that was turned in by Lewis Perkins.
A much-changed Harlow side controlled much of the possession, but were unable to turn it into clear-cut chances. Mario Noto and Lawrence Yiga forced Abbott's goalkeeper Lewis Lockyer into saves, but thevisitors were unable to draw level.
With the game drawing to a close, and Harlow searching for the equaliser, Romaric Logon broke from his own half on the counter-attack, finishing well to seal the win.