The Tykes had a golden opportunity to take a point back to South Yorkshire, when Ryan McLaughlin won a penalty with just under 10 minutes left.
But Chris O'Grady's spot-kick smashed the frame of the goal to deny them a draw which on the balance of play they would have deserved.
Bolton's on-loan signing Joe Mason was named among the substitutes in what was the last game of his loan spell before returning to parent club Cardiff.
Liam Lawrence returned for the visitors after missing their defeat by Burnley with a slight calf strain and Kelvin Etuhu came back from suspension.
Barnsley looked threatening early on and should have taken the lead. Terrific interplay saw McLaughlin feed the ball into Dale Jennings, who somehow blazed it over the bar.
Beckford then had a chance to open the scoring. Chung-Yong Lee cut the ball back inside from a cross, but the Jamaican international could not guide the pass to the target in a half that failed to capture the imagination.
But, just as the game was approached the break, Wanderers scored a surprising goal. A long ball out of defence from Matt Mills caught the Barnsley defence napping, with Beckford controlling well and then rounding the ball past Luke Steele into an empty net.
They then had the opportunity to double the lead early in the second half. Alan Hutton set-up Andre Moritz from close range, but Steele stood tall and chested the ball out for a corner
The Tykes had a chance to equalise when O'Grady volleyed from the edge of the area, though the ball went straight into the hands of Adam Bogdan.
A Rob Hall long ball puts Beckford into a similar situation from which he scored. However, this time he could not guide the ball home.
Barnsley were now pushing for the draw with chances from Kennedy and Tomasz Cywka and they could have had a penalty when O'Grady looked to be pushed in the back by Matt Mills.
McLaughlin had a great opportunity but his free header from three yards out was not on target. Jennings then hit a shot from 25 yards which smashes against the post, though the referee awarded a corner.
Their biggest chance came when McLaughlin won a penalty after being brought down in the box from a clumsy challenge from Alex Baptiste, who was then substituted shortly after.
But O'Grady's penalty hit the post and went out for a throw, with Bolton then holding on for the win