Putoko made a major break and was cut down inches short, but Hamilton continued to surge forward and after a couple more phases Putoko threaded his way through for a match-winning try which finally did justice to his team's massive superiority in possession and territory.
It was a cruel finish for Napier, who's smothering defence had otherwise largely nullified the attacking threat posed by Hamilton's backline stars.
Long-serving Hamilton coach Nigel Hotham called it "a classic final".
"The fact we won means we are delighted, because we have also had our share of heartbreak over the years," he said. ""Napier were very strong in the forwards and defended well on the edges.
"But there was always a real belief there that we could do it.
"This is a team that has demonstrated it does not give up. One turnover was all we needed, we knew from there we could always do something special."
For Hotham it revived plenty of historic memories.
"We've been in this situation before," he said, recalling how Hamilton Boys' needed Bryn Gatland to drill a drop goal a minute from fulltime to beat St Kentigern College – on a 60-match unbeaten run at the time - 12-10 in an equally heart-stopping 2013 final in Hamilton.
He also drew comparisons with Hamilton's stirring efforts to force a 26-26 draw and shared title with Wellington's Scots College in 2014 - until now his school's most recent title win - after being 19 points down
And a nervy 6-6 draw with Auckland's De La Salle College in 2008 thanks to two Kane Adams penalties.
However there was also much to admire in the 2022 final. George Manson had given Napier an 11th minute lead from following a maul and Cory Berkett – perhaps Napier's best player on the day - converted.
But Napier captain Max Ratcliffe was sinbinned six minutes later and before he could return McCarthy scored for Hamilton following a short lineout.
Napier fullback Joshua Augustine then gave Napier a 12-5 halftime lead after his team pounced on a Hamilton error.
In the 52nd minute Cory Berkett extended the lead to 15-5 with a penalty, but Hamilton skipper Aki Tuivailala scored a converted try in the 59th minute to give his team hope.
Hotham highlighted the individual efforts of McCarthy, who had the day's highest tackle count; Putoko, who had also scored a 90m try on the Friday; and Tuivailala, who he called "a superb player and a superb person".
And he also noted the efforts of flanker Oli Mathis, who came off the bench after having been in a moonboot with a high ankle sprain for most of the week.
Hotham said there was tremendous respect between Hamilton and Napier and the teams shared hongis and hakas after the game.
Hamilton also finished the season with the Moascar Cup, the Ranfurly Shield of schoolboy rugby, which was also on the line.
Meanwhile the national girls title was shared between Manukura and Christchurch Girls High following a 19-19 draw, after Manukura had earlier led 19-0.
