Watson slotted an excellent goal from an acute angle, capping a dominant first half on Thursday night at Marvel Stadium.
But the umpire ruled that Watson had run off his line when he took the kick, meaning the score did not count because it was taken after the siren.
The AFL stood by the decision on Friday after Hawthorn said they would seek an explanation.
"The umpire, positioned directly behind the kick, correctly disallowed the score after Nick Watson moved off his line to the right and didn't kick the ball over the man on the mark," the AFL said in a statement.
"The AFL have contacted Hawthorn and St Kilda today to provide an explanation regarding the decision."
Watson bit his tongue post-match, with coach Sam Mitchell saying the decision didn't make sense.
"We'll certainly be going to the AFL to ask about it ... there's no common sense about that," Mitchell said on Thursday night.
"When something doesn't make sense, they fix it pretty quickly. Why would he run wider, to give himself a harder shot?"
Watson similarly was unimpressed that the goal was disallowed.
"Don't get me started ... they're pretty keen to get the whistle out," Watson told Kayo Sports.
"Actually I won't say anything about the umpires, I might get a fine."
It was one of few things that did not go right for Hawthorn as they cruised to a 52-point win. They kept the Saints goalless until early in the third quarter.
Will Day made it through his first game of the season unscathed, and they could afford to rest Jack Gunston for the last quarter after he also returned from injury.
Gunston had kicked five goals to three-quarter time. Blake Hardwick took his spot in attack and kicked another four, prompting plenty of mirth on the Hawthorn interchange bench at Gunston's expense.
"It was just mainly about how easy it is to play his role - that's what all the other players were saying to him (Gunston)," Mitchell said.
"Blake is a real favourite of all the boys, so when he's down there kicking goals, they really enjoy that, to take the micky out of Jack."
Day had a dislocated shoulder in the pre-season, continuing his bad injury run and sidelining him until Thursday night.
He said it had been tough, but the star midfielder has gained fresh perspective.
"I just got to work, learned a lot about myself, and now coming back I've got a new mindset and I had a lot of fun (against St Kilda)," Day said.
10°C