Barnet had dropped into the npower League Two relegation zone at one stage during the afternoon, with Hereford beating Torquay, but Hughes made sure his side survived by popping up with a 60th-minute winner at the Pirelli Stadium.
The Bees made a dream start when full-back Mark Byrne, a former Burton player, saw his 25-yard free-kick take a big deflection to beat home goalkeeper Ross Atkins after only six minutes. But Burton, whose victory over Macclesfield last weekend sent the Silkmen into non-league, went on to dominate the first half.
The hosts were back on level terms in the 27th minute when midfielder Jacques Maghoma fired home from the edge of the box after linking with striker Calvin Zola. And Zola could have added to the concerns of the 800 travelling Barnet fans in the 43rd minute, but he blazed a penalty wildly over the crossbar after being pushed to the ground by Byrne.
The Bees sent on injured top scorer Izale McLeod for the second half but it was Sam Deering who should have put them back in front in the 51st minute. However, Deering could only shoot wide from close range after a Ben May header had been blocked on the line.
But the pendulum did swing back in the favour of Londoners when skipper Hughes squeezed home a left-footed volley from the edge of the area to extend Barnet's stay in the Football League.