Barnsley led going into the final minute when Rob Kozluk headed into his own net. Extra time looked likely but in injury time Reading gave away a penalty and Daniel Bogdanovic stepped up to score his 2nd of the night.
It was a poor evening for Reading who learned that Tommy Smith had been snatched from their grasp by Portsmouth. A deal is expected to happen soon with Pompey.
Reading have a chance on Saturday to exact their revenge on the Tykes when the teams meet at Oakwell in the Championship.