The Bluebirds led the Tykes 1-0 heading into the closing stages of a midweek clash in South Wales, with Ben Turner's strike seemingly set to send them further clear at the Championship summit.
They were, however, hauled back by relegation-threatened Barnsley as Stephen Foster pounced in the 97th minute.
Mackay was surprised to see so much time added on at the end of the game, but has accepted the explanation offered by referee Fred Graham.
He said: "I wanted the referee to clear that up, which he did. The extra time was for (Cardiff defender) Kevin McNaughton going down (for treatment).
"I was surprised it was five minutes at the end of the second half, but it was and I just wanted to clarify where the extra time came from, and the referee did that.
"When they scored there was four seconds to go, he was going to blow the whistle four seconds later and I am absolutely fine with that."
Cardiff remain six points clear at the top of the table, nine in front of third-placed Watford, and require seven points from their remaining five fixtures to secure promotion to the Premier League.
Mackay added: "I was delighted with how we played, we were playing a team fighting for their lives. David (Flitcroft) has them working very hard and they have outworked teams to death.
"Tonight that did not happen. We dominated and we had chances.
"We could have been more clinical and finished the game off. At 1-0 anything can happen, including a freak goal."