Hosts Colchester dominated the early exchanges but things turned against them when they lost their keeper and also went down to ten men midway through the first period.
Dean Gerken was sent off for a professional foul after appearing to hold back Barnsley striker Kayode Odejayi inside the box.
Suddenly the U's were down to ten men and manager Geraint Williams was forced to send on teenager Mark Cousins as the substitute keeper for a surprise senior debut.
Cousins' first job was to pick the ball out of the net as Brian Howard beat him from the spot.
Yet battling Colchester, despite having to play with ten men for nearly three quarters of the game, were deservedly level just before the break.
Teddy Sheringham, making his competitive home debut for the Essex club steered home a precise cross from George Elokobi from close range.
Three minutes into the second half and the home side went ahead when wing-back Rob Kozluk headed into his own net, while under pressure from Matthew Connolly following a corner by Johnnie Jackson.
Barnley looked a beaten side when they too were reduced to ten men as skipper Paul Reid was dismissed for elbowing Sheringham in the 51st minute.
The U's looked comfortable, but they didn't bargain for referee Mr Hall awarding a harsh penalty with five minutes remaining.
Jackson blocked a fierce shot from substitute Kim Christensen at point-blank range. The ball appeared to hit him at the top of his shoulder, but referee Mr Hall considered it to be a hand-ball and gave the Tykes a lifeline.
Up stepped the reliable Howard to dispatch his second spot-kick of the afternoon, sending rookie keeper Cousins the wrong way.
Both sides could have won it in a hectic finale. Barnsley's Hungarian international Istvan Ferenczi sent a free header wide, while Colchester skipper Karl Duguid fired wide from a great position.