The Bees started nervously and Chester should have capitalised on Barnet's apparent lack of confidence in the sixth minute.
Poor concentration from the Bees allowed Gregg Blundell to steal in behind their defence, the former Tranmere Rovers striker selflessly cut the ball across the six-yard box to Jon Walters, but he somehow contrived to miss the ball with an open goal from five yards.
Barnet's response took ten minutes to arrive and lacked any real quality. Nicky Nicolau combined well with Nicky Bailey, while Dean Sinclair was free with time and space at the back post, but Nicolau's cross cleared the entire penalty area.
In the 19th minute Ross Flitney brilliantly punched clear a dangerous Roberto Martinez free kick with three Blues players waiting to pounce. Nicolau picked up the clearance and put Sinclair clean through with a 40-yard pass.
The former Norwich City midfielder raced in on goal and curled his shot towards the bottom corner from the edge of the area. The crowd jumped up to celebrate but John Danby somehow managed to tip the ball around the left-hand post.
While Barnet may have lacked guile they were good value for their lead in the 30th minute.
Kevin Sandwith dragged down Sinclair, and referee Lee did not hesitate in pointing to the spot. Sinclair sent Danby the wrong way coolly slotting into the right corner.
Chester nearly grabbed an equaliser in the 44th minute when Dean Bennett bundled his way past two sloppy Barnet challenges and fired in from six yards. However Flitney produced a stunning point blank save to deny him a certain goal.
With both sides working hard for little reward, Bailey could have won the game for Barnet from the penalty spot at the start of the second half, after Phil Bolland tripped Ismail Yakubu. But he went for power and was denied by a good low dive from Danby.
Chester should have equalised a minute later when Bennett crossed to Walters at the far post, again three yards out he managed to miss this time with his head, giving Barnet all three points.