The Bluebirds dominated proceedings but only held a 1-0 lead thanks to Ben Turner's 59th-minute strike. A minimum of five additional minutes was signalled by the fourth official, but Stephen Foster earned relegation-threatened Barnsley a valuable 1-1 draw as his shot wrong-footed David Marshall in the 97th minute of the game.
Mackay 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."
He added: "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 dominated proceedings and ought to have been further ahead prior to Foster's goal, with Craig Bellamy hitting the post and Heidar Helguson wasting two golden opportunities. Despite the setback, Cardiff's promotion still appears a formality as they now lead third-placed Watford by nine points with five games remaining.
A haul of seven points from those fixtures will guarantee Cardiff a Premier League place, regardless of other results, but Mackay, while pleased with his side's performance, admitted his side should have made more of their opportunities and put one foot in the Premier League.
He said: "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. That did not happen."
The draw continues Barnsley's fine recent run under Flitcroft and they have now lost just once in their last seven league games.
The point moves them two clear of the drop zone ahead of Saturday's meeting with Charlton, and Flitcroft believes the result has given them a great boost at a crucial time.
He said: "That is more than a point for us. To fit this game into our programme after the game against Crystal Palace and after Easter week, it was asking a lot of this group. But you cannot ask for more than going 97 minutes against the champions-elect. This gives us real momentum and confidence ahead of the Charlton game."