Two-time winner Chris McCormack did not race because of illness.
Three-time winner Craig Alexander and defending champion Pete Jacobs were more than 20 minutes off the pace early in the marathon.
Carfrae was on track to continue Australia's seven-year winning streak at this race, which started when Michellie Jones took out the 2006 title.
She was eight minutes off the pace after the bike, but quickly started making up time.
Carfrae stormed into the lead at 24km, effortlessly passing Great Britain's Rachel Joyce.
There was no repeat of last year's stunning setback, when she was on the verge of taking the lead.
She suddenly ran out of energy and struggled to third place.
Van Lierde is no relation to compatriot Luc Van Lierde, who won Hawaii in 1996 and `99.
Frederik was third last year and came to Hawaii on the back of a consistent season.
"I believed I could do it - the belief was there and I've worked hard this year. I've never worked so hard,'' Van Lierde said.
McKenzie collapsed at the finish and was taken away on a stretcher, but he was ecstatic.
His previous best at Kona was ninth two years ago.
Last year, he slid to 24th but, this June, he dominated at Ironman Cairns for his sixth win over the distance.
"Fred was just too strong, but that was a dream to lead the Hawaiian Ironman like that,'' McKenzie said.
"I'm a little bit disappointed not to hold on to the win, but seriously, second - I will take that.
"That's the best day of my life.''
McKenzie, 32, shared the lead with American Andy Starykowicz for much of the 180km bike ride.
Starykowicz broke clear in the last few kilometres as the wind picked up and had a 59-second lead at the start of the run.
McKenzie quickly moved to the front and built a lead of more than two minutes.
But Van Lierde, who was fourth off the bike, never let the Australian move too far ahead.
The Belgian took the lead before 30km as the Australian started to struggle.
Jacobs and Alexander faded dramatically on the bike and were more than 18 minutes off the pace at the start of the marathon.
Alexander had a flat tyre before he had even ridden out of Kona at the start of the bike but, fortunately, a neutral spares van was immediately behind him.
-AAP