Harry Wheeler’s men took the lead on 27 minutes through Blair Turgott before substitute Gold Omotayo made sure of the three points in the second half.
The result means The Bees stay 12th, eight points off the play-off places.
It was the visitors who created the first chance of the game on 11 minutes. Jack Paxman nicked the ball off Charlee Adams before bursting forward, hitting the ball low and hard, forcing Mark Cousins to get down low to save.
The Bees hit back moments later though when Cheye Alexander twisted and turned a defender before letting fly from distance. However, his stunning drive from the edge of the area was well saved by Grant Smith in the Maidstone net.
Elliott Johnson’s free-kick on 23 minutes looked to be dipping into the top left corner but it was well caught by the ‘keeper.
Despite pressure from The Bees, it was Maidstone who hit first on 27 minutes. Turgott was played through on goal before slotting comfortably past Cousins.
However, the Barnet shot-stopper was on hand to deny the goal scorer a second just before half-time, a fantastic diving save kept out his bending effort.
Cousins then got down low to deny Elliott Romain at the near post to prevent the visitors from taking a two-goal lead into the break.
The Bees’ goalkeeper was called into action yet again 11 minutes into the second half. After Romain set up Paxman just inside the box, his shot was well kept out by Barnet’s number one who got down low to keep the score 1-0.
Jack Taylor then found room to let fly but his speculative effort whistled over the bar and the South Terrace.
With 15 minutes remaining, Maidstone had another chance to double their lead. After some brilliant counter attacking play from Turgott, he found Omotayo but his shot was well blocked by the feet of Cousins.
Soon after, Shaq Coulthirst became the first name in the referee’s book for simulation seconds before Alexander tried his luck from distance but it fell wide of the post.
The miss proved costly as Maidstone bagged their second with just over 10 minutes to go. Jake Cassidy’s initial shot was saved but Omotayo was on hand to poke home the rebound.
Despite two late headed efforts from Ephron Mason-Clark and Jack Barham, the visitors managed to hold on to claim a vital three points.
John Still’s men return to action next Sunday when they host Bristol Rovers in the First Round of the FA Cup.
Barnet Starting Line-up: Cousins, Alexander, Johnson, Reynolds (C), Robson, Tarpey (Barham), Adams, J.Taylor, Fonguck, Walker (Coulthirst), Tutonda (Mason-Clark).
Unused Subs: Matrevics, Sweeney.
Attendance: 1,424 (339 visitors)