With scores locked at 14-14 and 70 seconds left in golden point at Allegiant Stadium, Dragons prop Ryan Couchman was penalised for a strip on Bronson Xerri.
From the penalty, Bulldogs captain Stephen Crichton stood up at the crunch, nailing a field goal with six seconds to play to deliver the Bulldogs a famous victory.
But Flanagan was left disappointed in the aftermath, adamant it had been a loose carry and that Couchman had not stripped the ball when his arms bounced back in the tackle.
"It's a loose carry. Every day of the week. Without a doubt," Flanagan said.
"We didn't get the rub of the green that's for sure. Disappointing, but it wasn't decided in my view the right way.
"The game has been put on a real high pedestal. I just thought tonight it shouldn't have been decided the way it was.
"The NRL has done a great job, the club has done a great job.
"The fans will decide. Good luck to the Bulldogs, they were good enough to win and kick the field goal. That's skill.
"But I think we should have gone home one point each."
Canterbury coach Cameron Ciraldo insisted afterwards he had not had a proper look at the call, but also pointed to several decisions he was unhappy with.
In the end, though, it was fitting that Crichton delivered, having become one of the NRL's best clutch players on the big stage.
"It looked like it was tracking towards a draw there and one point each," Ciraldo said.
"Both sides deserved that but credit to (Crichton), he has worked really hard on that and he deserved to get one on the big stage today."
With 45,719 in attendance at Allegiant Stadium, this was easily the best NRL match played on US soil so far.
The Dogs led 10-8 at the break and went further ahead with a try to winger Jacob Kiraz after a trademark Crichton left-hand flick.
Dragons debutant winger Setu Tu, at the age of 27, capped a stellar match with a try in the 59th minute to reduce Canterbury's lead to just two.
The Red V defended like demons to scramble and deny the favourites on numerous occasions.
With Valentine Holmes limping, Kyle Flanagan nailed a 30m penalty and it was 14-all with six minutes on the clock.
In the first segment of golden point, Jaydn Su'A charged down a Matt Burton shot. Connor Tracey did the same to deny Daniel Atkinson, while Valentine Holmes had another crack from 45m that failed.
Atkinson went for a failed 50m shot with 90 seconds to go and the Bulldogs received a penalty.
Crichton then stood up to cap a man-of-the-match display.
The two sides have a fierce rivalry and there was niggle and flair-ups, particularly when Crichton caught Tu high in the first half, with Flanagan also indicating he felt the Bulldogs captain should have been sin-binned.
The other good sign for the Bulldogs was the form of half Lachlan Galvin, who has cleaned up his passing precision and decision-making after a full pre-season at the club.
The 20-year-old spied a chance on the right side to set up the Bulldogs first, when he skipped across and threw a slick pass to put storming back-rower Jacob Preston through.
The Dragons hit back with creative hooker Damien Cook dinking a slick left-foot grubber through for rampaging prop Emre Guler to plant it.
After the break the Dragons blew up when Moses Suli went off for an HIA after they claimed he had been head-slammed by Bailey Hayward.
They were penalised for dissent and Crichton made them pay with a try-assist and the magic moment at the death.
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