Steve Morison clinched victory on Saturday with a second-half header but Millwall had to endure seven minutes of stoppage time before celebrating only their second Sky Bet Championship away win of the season.
Morison was denied a second by a brilliant save from Lee Grant and Derby skipper Richard Keogh twice headed wide from good positions but Millwall defended superbly and deserved the win that boosts their hopes of avoiding relegation.
Derby fans were furious at what they saw as time-wasting by the visitors but Holloway mounted a strong defence of his players.
"I have to say I think it's bizarre," he said. "I've got two of my back four on the bus who won't play on Tuesday but I'm being criticised for them being on the floor.
"What on earth can I do about that if they've been kicked? Yet some of the fans said I was telling them them to lie down. Never in a million years would I encourage anybody to be anything other than a brilliant professional and work hard and be honest and true.
"I saw some really strange decisions out there as an away manager and I think the referee's overall performance was bizarre. I'm going to have a chance to complain about his performance with some marks."
But Holloway also had plenty to say about his team's display which he wants to be a marker for the rest of the campaign.
"I want us to grow in belief and now we have got 12 cup finals left and I want to get promoted to the Championship because I don't like relegation battles," he joked.
Derby head coach Steve McClaren had no excuses for the shock defeat which has dealt a blow to his team's chances of automatic promotion.
"I think if we had been playing for two more days we wouldn't have scored," he said. "We had no quality in the final third and chances and half-chances that we normally take we didn't.
"They came to do a job and they frustrated us and frustrated the crowd and in the end took the three points away.
"There's not been many times when I've said I've been disappointed with the performance but today is one when I can.
"That's only five goals in the last three games which is a little bit worrying and I think teams are coming here, parking the bus, making it difficult and we didn't today have the quality to get the goal.
"Opponents are going to come here and frustrate us and we have to deal with that but we didn't deal with it very well."