The Hawks were without Clarkson for five matches during the season after he was admitted to hospital with Guillain-Barré syndrome, and the club's woes were compounded by injuries to several key players during that period.
With assistant coach Brendon Bolton at the helm, the Hawks won all five games without Clarkson and the 46-year-old said this epitomised the spirit at the club.
"We had to confront a fair few challenges over the course of the year both as a playing group, in terms of the injury toll at different stages, especially to key players, but also to the coaching group", Clarkson said after the victory.
"To overcome them and get a victory on grand final day is a very, very special feeling for our footy club."
The Hawks were at their tenacious best for all four quarters on Saturday, something few sides have been able to do against the Swans all year.
Going into quarter time, the Hawks led the tackle count 22-7 and were well and truly on top, with Clarkson saying it was a testament to the hard work his players had done throughout the year.
"The result didn’t come as a surprise to us. I don’t mean to say that in an arrogant fashion, we just prepared so well," Clarkson said.
"It was pretty tight early but I was really pleased with our attack on the ball and our attack on the Sydney players when they had possession of the footy. Our tackling was first grade and that enabled us to get some opportunities in the front half."
"What was more remarkbale about that was that Sydney only had seven (in the first quarter). Sydney are a side that are very, very aggressive in the tackle and are very, vey good at it. Usually they're the side that has 20 to 25 tackles in a quarter."
While they have won three flags in the past seven years, it hasn't always been easy sailing for the Hawks in September.
A tough three point loss to Collingwood in the 2011 preliminary final was followed by grand final heartbreak at the hands of Sydney in the following year.
Captain Luke Hodge, who celebrated his 250th game with his third premiership win and his second Norm Smith medal on Saturday, said these previous disappointments were a huge motivating factor in this year's win.
"We’ve got a lot of competitive people in our side. It wasn’t only the 2012 loss, it was the 2011 preliminary final loss (to Collingwood), it was the 2007 loss to North Melbourne that still rings in the guts of a few of the guys, ones that you let slip," Hodge said.
"They are all motivational factors, I believe. The feeling you get after a finals loss knowing your seasons over after it's finished, it sits in your guts for a long time.
"And you can see by the attitude of the guys today (how these losses motivated us). From the first bounce, we were ferocious at the ball and at the opponent and that showed how ready we were to play today."
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