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Iain Hume and Stephen Foster grabbed the goals after heroics from home keeper Luke Steele.
As Derby looked for an early opening Miles Addison cashed in on a mistake by Diego Leon and founds gap to produce a long-range effort, but his wild shot was wide.
And when a free-kick gifted the visitors an opportunity Paul Connolly smashed the 20-yarder over.
A slick move from Barnsley almost caught out Derby when Rob Kozluk's pinpoint pass found Martin Devaney and his low cross reached Jon Macken, but his sharp shot on the turn was blocked.
Derby continued to shoot from long range and a Paul Green shot after 23 minutes drifted wide before Przemysław Kazmierczak's 25-yarder was wide.
Mounir El Haimour hit another optimistic shot wide before aiming a pass into the middle for Diego Leon, but he volleyed high over he top from the edge of the area.
Three minutes before the break Derby might have edged in from when Green cut in from the right and hit a left-foot shot, but Steele dive full stretch to his left and turned the shot away.
But as Derby stepped up the pressure midway through the second half Steele became Barnsley's saviour with a string of crucial saves.
Former Sheffield United striker Rob Hulse drilled a dangerous low shot that almost crept through a crowd.
But after 64 minutes Steele was the home side's hero. Kris Commons produced a quality shot out of the blue from outside the area, but Steele managed to parry it away.
And when Kazmierczak followed up smartly Steele managed to block again this time with his legs.
Three minutes later Commons was on target again three minutes later only for Steele to palm away the chance and when striker Emanuel Villa got in on the act, Steele was in the way again.
But after 71 minutes Derby and their 2,900 fans were stunned with a super strike from Barnsley's first shot on target.
A Brian Howard free-kick was headed out of the area before Hume lashed in a fabulous volley.
Barnsley's second came with a well worked set-piece. Hume's corner was aimed perfectly and Foster charged in unchallenged to power in a super header to put the result beyond Derby.