The 17.10 (112) to 16.4 (100) victory ensured the Hawks will finish atop the ladder and host the Swans in a qualifying final next Friday night at the MCG.
Jarryd Roughead kicked four goals to put one hand on the Coleman medal and Sam Mitchell was at his indomitable best, but in terms of next month nothing mattered more than a single undisciplined act from Franklin.
There's every chance the talented 26-year-old will be suspended for at least one match after being reported for making contact with Nick Malceski's head in the second quarter.
A 2012 rule change means the key forward has no carry over points despite being suspended seven times, but his bump was late and came after Malceski kicked the ball.
Several Swans rushed to remonstrate with Franklin, who is believed to be weighing up a $10-12 million Greater Western Sydney offer and has put contract talks on hold until the end of the season.
Malceski left the field groggy and was substituted out of the game in the final quarter.
The Swans' medical report will help shape the verdict of the match review panel, who face a tough ask in determining if the bump was negligent or reckless.
Regardless, Franklin's actions were unnecessary and came over two years after he vowed to wipe the bump from his repertoire.
"I've just got to take it out of my game. I'm missing games because of that," Franklin said of his 2011 one-match suspension for a high bump on Gold Coast's Maverick Weller.
Franklin kicked two goals on Friday night, with Roughead starring in the visitors' come-from-behind win.
Roughead now has 68 goals for the season, with second-placed Travis Cloke now seven behind on the AFL's goal-kicking table.
Sydney led for most of the night after Jesse White kicked the game's opening goal, and were up by 26 points in the second quarter.
Fittingly, it was Roughead who finally gave the Hawks the lead in the third minute of the final term when he popped through his third goal.
The reigning premiers, who will enter September with one win from their past four starts, fought hard in the final term but never recovered from the Hawks' final-quarter blitz of five goals in 13 minutes.
The undermanned Swans, minus nine of their premiership 22 from last year's grand final between the two sides, were further weakened by the late withdrawal of star recruit Kurt Tippett due to a tight hamstring.
Hawks coach Alastair Clarkson suggested Franklin's bump was not a "very malicious act".
"He's been reported. We've just got to let the authorities deal with it and we'll see what happens," Clarkson said.
"It is what it is. We've won games of footy without him in the past."
Swans coach John Longmire said he hadn't seen a replay of the incident but that there were a lot of positives for his side in the defeat.
"82 tackles. In the first half in particular, our ability to cause turnovers and score from those turnovers was good," Longmire said.
Longmire expected Tippett, Dan Hannebery (knee) and Nick Smith (calf) would all be right to return next weekend.
HAWTHORN 2.2 7.5 11.6 17.10 (112)
SYDNEY 5.2 9.2 13.4 16.4 (100)
Goals: Hawthorn - Roughead 4; Gunston, Breust, Franklin 2; Lake, Hale, Birchall, Anderson, Lewis, Puopolo, Mitchell. Sydney - White, Parker 3; Rohan, Mumford 2; McGlynn, Bolton, K Jack, Morton, Pyke, Mitchell.
Umpires: Brett Rosebury, Shane McInerney, Dean Margetts.
Official Crowd: 37,980 at ANZ Stadium.