Scott Malone's injury-time equaliser rescued a point for the relegation-threatened Lions, who hit back after Charlie Austin's 77th-minute spot-kick.
Austin had scored from the spot after Simeon Jackson handled the ball on the edge of the area.
Holloway said: "I think handball should be deliberate. It might have hit his hand but was it in the box and was it deliberate?
"If there hadn't been a whistle, not one person behind that goal would have jumped up looking for a penalty - and I know this ground pretty well. I can't believe what I saw.
"I've had the benefit of watching it six or seven times, but even when watching it in real speed I thought it was harsh.
"The ball was not going to be headed in and my player was on the edge of the box, if he was even in it. I just don't understand.
"But because it's Millwall it doesn't matter. How many times has that happened this year?"
Millwall, who had won their previous three away matches, must triumph in their final match of the season, at home to Bournemouth, to be sure of their Sky Bet Championship survival.
They created a number of first-half chances at a ground where former QPR player and manager Holloway remains a popular figure.
"I thought my lads were absolutely fantastic from start to finish," he added.
"They've been superb for me over the last couple of months and I really couldn't ask for any more. At least it's still in our hands."
QPR boss Harry Redknapp, whose team were already certain of a play-off place, admitted: "When you're 1-0 up in the last minute you expect to see the game out.
"It's difficult to balance a team and maybe we had too many players who are good when they have the ball and not so good when they haven't got it.
"When we didn't have possession we didn't close down as well as I would have liked. It's about finding that balance and a happy medium and that's what we've got to do for the play-offs.
"Wigan lost which means we know we're going to be at home for the second leg and that's what we wanted rather than the other way around."
Of the penalty incident, he added: "I haven't seen the replay, but everyone who has seen it says it was a penalty.
"Millwall played well. They've got bags of enthusiasm and have had some great away results recently, so they've been in good form."