Manager David Dunn was left disappointed as Kevin Long’s late strike meant Latics’ three game unbeaten run came to an end.
Mark Yeates equalised for Athletic with 12 minutes of the game remaining, after Conor Hourihane gave the Tykes the first half lead.
With Latics the likelier of the two sides to clinch victory in the final minutes of the game, Barnsley loanee Long smashed home the winner in the 90th minute.
Speaking after the game, Dunn said: "In the first half I don’t think we really turned up. We gave ourselves a hell of a lot to do with the first half performance. We were second to everything, gave the ball away and was in our shells.
"But to come out second half, I thought we were much better and if one team was going to win it, it was going to be us. Sometimes this game kicks you where it hurts sometimes and it’s disappointing but we’ll go again.
“I thought Cammy [Dummigan] did well on his return but as a team I don’t think we can afford to be playing in 45 minute periods which, possibly, we got away with it at Chesterfield. Mansfield was similar where we seem to be doing better in the second half so that’s something we are going to have to address.”
The game, however, could have been a lot different if the referee had awarded Latics a first half penalty as Yeates appeared to be fouled in the box.
“I’m not going to come out and criticise anyone but the answer I got was that it was normal contact,” admitted Dunn. “I don’t know what that means but I’ll have to go an ask him in a minute.
"For me, if there is any contact in the box and the defender doesn’t get the ball then I think that’s a penalty. Certainly if he’s in the box and he’s gone past him. If there is contact, I would have thought that is a penalty.”
Athletic can now quickly look to the game with Southend United on Tuesday night. “One thing in football is that you get a chance to put it right pretty quickly,” said the 35-year-old.
"There is no quicker time to do that than Tuesday. As much as I’m disappointed I am right now, it’s important we regroup and get them all ready for Tuesday where it’s another game we can win.”
Watch the full interview on Latics PlayerHD.