With Blackburn 2-1 up, Atkinson then failed to spot a push from Gabriel Agbonlahor on captain Ryan Nelsen, allowing former Rovers defender Stephen Warnock to rifle the home side level.
From that moment the momentum shifted Villa's way, and when James Milner scored from the spot 10 minutes later after Chris Samba was dismissed for a foul on Agbonlahor, the writing was on the wall for Blackburn who went on to lose 6-4 on the night and 7-4 on aggregate.
"It's a bit difficult to take, scoring four goals and not getting through to the final," reflected Allardyce.
"We were in complete control of the game, and if anybody was going to score again it was us.
"But then the referee allows a blatant foul on Ryan Nelsen to go unpunished, and at this level you have to make sure the referee gets those decisions right.
"We are out of a cup final because of that decision perhaps. It is a major decision that has stopped us having the chance to go to Wembley.
"Whatever anybody might say, we were put in a position we should not have been put in.
"It lifted the crowd, it lifted Villa because they were playing very poorly, and then they are on their game.
"You could look at the fourth goal and say Agbonlahor had two arms on it and deflected it into the net for 4-2.
"Everybody thinks it's over, we're down to 10 men anyway, but then we managed to get back to 5-4.