The Rams looked like they were going to be beaten by Chris O'Grady's 47th-minute strike despite having dominated the first half.
But right-back John Brayford popped up just in the nick of time to level with a 90th-minute header and earned the visitors a welcome point.
"I thought we thoroughly deserved a point but it really should have been three after the first-half performance," said Clough.
"Our defence has been absolutely superb and we limited Barnsley to just one or two shots all game.
"But the players are extremely disappointed with their goal because there was a blatant foul in the lead-up to it.
"However, on the back of two defeats, I'm really pleased with the effort of the players."