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 after the siren.
Watson bit his tongue post-match and coach Sam Mitchell said they would go to the league about the contentious call, saying it 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
"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 goal-less 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 Hawks 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)," he said.
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