The Eagles were out of the blocks quickly and silenced the vast majority of a sell-out crowd through Mile Jedinak's fourth-minute opener.
But the Welsh hosts asserted themselves and were level just before the interval when Craig Noone finished neatly, and substitute Aron Gunnarson completed the comeback by netting a Bluebirds winner 17 minutes from time.
"We started well and ended terribly," said Holloway, whose side could have moved to within a point of their hosts with victory.
"I thought we stopped creating chances and in these games you can't do that and you have to keep going. It was as simple as that.
"You know with this crowd like it is Cardiff are going to come back and in the end I am bitterly disappointed in the last 15 minutes because if any side looked like they were going to score a goal it was Cardiff.
"After they scored I don't think my team did what they needed to do, in fact they did worse and not better.
"There was a lot about us that I was delighted with but I just didn't like the way we ended the game. We have got to look at that part of ourselves because that could be crucial come the end of the season."