Town suffered a first defeat in six at The Hive on Tuesday night as Dave Tarpey's first Barnet goal seperated the sides.
Simon Weaver's side pushed for an equaliser, but were kept from geting on the score sheet for the first time since December and returned home empty handed.
Simon Weaver named the same starting line-up for the sixth consecutive match, with the only change coming on the bench as Michael Woods replaced Aaron Williams.
Both sides best chances fell to defenders in the opening five minutes as Warren Burrell headed George Thomson's corner wide, before Elliott Johnson fired over at the other end.
Burrell was then in action at the other end as he was forced into hooking a powerful header off the line to prevent his side falling behind.
The opener arrived on the half hour mark as Ephron Mason-Clark was sprung in behind the Town defence from where he was able to pull back to Tarpey, who dispatched his first Barnet goal past James Belshaw.
Town rallied late in the half in an attempt to go into the break level, though Thomson's low drive was cleared away before, on the stroke of the half, Kelvin Langmead's header was caught by Cousins.
Burrell again demonstrated his aerial threat in the first action after the restart, guiding Thomson's free kick towards the top corner, but not out of Cousins' reach.
Barnet soon reminded Town of their threat on the counter attack as Wesley Fonguck's drive deflected for a corner, ten minutes before Shaquile Coulthirst should have doubled his side's lead, but headed past the post.
Joe Leesley was introduced as Weaver tried to change things around and find an equaliser, but the winger's first involvement was to see a well struck volley blocked.
James Belshaw went up for a corner in the dying seconds and was almost on the end of Leesley's corner, but it wouldn't drop for Town who were shut out for the first time since December and travelled home empty handed.
Harrogate Town: Belshaw, Fallowfield, Falkingham, Howe, Burrell, Thomson (Woods 83), Emmett (Leesley 74), Beck, Langmead, Kerry, Muldoon
Subs not used: Senior, Cracknell, Agnew
Barnet: Cousins, Alexander, Johnson, Reynolds, Tarpey (Akinola 77), Coulthirst (Sparkes 65), Taylor, Boucaud (Robson 65), Fonguck, Sweeney, Mason-Clark
Subs not used: Azaze, Barham
Goals: Tarpey 30
Referee: D Rock
Attendance: 849 (90 away)