Villa trailed at half-time on Wednesday night and looked out of sorts when operating with a 4-3-3 system.
But Houllier altered his formation for the second 45 minutes, brought on Heskey and saw a dramatic lift in Villa's fortunes.
Heskey scored within 60 seconds of entering the action and had a hand in the build up to both goals from Ashley Young.
Houllier said: "I know what Emile can do. He showed a few things in training to indicate he was in good form.
"He was decisive. With Emile, it's a matter of confidence. It's the same with all strikers but probably more so with him.
"He knows I like him. I signed him for Liverpool. John Carew probably tired out the Blackburn defenders.
"Emile came on and was showing freshness, scored one goal and played a part in the other two."
Houllier added: "I was not disappointed by the effort and application in the first half but there was no flow to our game.
"I changed the system for the second half and it suited the players more, the way we played."
Blackburn boss Sam Allardyce was disappointed to see his side again fail to hold on to a lead.
He said: "We've gone in front in six games out of seven and haven't been able to hold onto things.
"A game lasts 90 minutes, not 45 and it's frustrating for us.
"We couldn't cope with Villa's change in shape.
"We must be more resilient defensively and just keep working away at things."