The youngster netted six minutes after half-time to add to David Poole's opener and ensure the Bees headed south with nothing to show for their efforts.
It was another day, another formation for Jim Gannon and his Stockport side, as the manager again made a clutch of changes in an attempt to get back to winning ways following back-to-back defeats.
After a pedestrian opening spell, Stockport had the first sight of goal after 12 minutes. Tes Bramble was upended just outside the box, but recalled skipper Tony Dinning curled the free-kick just past Lee Harrison's right-hand post.
The visitors replied with a header wide from Tresor Kandol, but both sides were having problems in front of goal in the opening quarter of the game.
Le Fondre sent in a tempting cross for Bramble on 25 minutes, but the County frontman disappointingly blazed high and wide.
The deadlock was broken just after the half-hour mark, and it was Stockport who grabbed a deserved lead.
Dinning played in Bramble, his low drive was blocked by Harrison, but the ball fell to loan man Poole who rammed home his first Hatters goal.
The opener clearly lifted Stockport, and within minutes of taking the lead they went close through Jason Taylor, Adam Proudlock and Poole again.
The small but vocal travelling support tried valiantly to rally Barnet, but Paul Fairclough's men continued to struggle to create an opportunity of note.
Stockport doubled their lead soon after the restart with a goal of high quality.
Barnet defender Anthony Charles produced a poor clearing header, and Le Fondre punished it by dramatically firing home the loose ball with an acrobatic overhead kick.
The home side were rampant, and minutes later Adam Griffin saw a sweet shot well saved by Harrison.
Barnet almost hit back on 56 minutes, as Kandol's looping header bounced back out off the crossbar.
That was about all the visitors could muster though, as Stockport eased home.