Border were further hampered when they lost both their dangerous midfielders Renato Tikoilosomone and Poasa Waqanibau to the sinbin for high tackles, playing 20 consecutive minutes with 14 men.
Then the Pirates' other pillar, No8 captain Lasa Ulukuta, showed his strength to reach out around the legs of his tacklers and score following a dash from a 5m scrum for 20-0 after 50 minutes.
The scoreline reflected the contest to this point, but having done themselves no justice, Border suddenly came alive and began to play their game.
First, determined winger Tom Symes was sole chaser on a misdirected kick and managed to trap both dangerous Pirates winger Pene Ulukuta and fullback Samu Etuati with tackles.
Finally getting some territory, Border kept the pressure on and after No8 Ray Stark and Horrocks went close, Tikoilosomone redeemed himself as he just paint-brushed the tryline with the ball amid a sea of black jerseys.
Forsythe and Waqanibau swooped on a midfield Pirates fumble to get them back to the line, with Pirates winger Clive Stowers being sinbinned for a professional foul.
Border struggled through a series of lineouts as Pirates tried to spoil each one, but they finally got the ball free for a perfectly-worked spread as flanker Kieran Hussey popped it up for Forsythe, in turn sending it wide to Waqanibau, who also redeemed as he bumped off his tacklers to slide over.
It was all Border as Pirates looked rattled, missing touch on a free kick, while Hussey and reserve lock Jack Hodge snatched back some priceless turnovers.
Middleton was suddenly everywhere and he sent the ball wide to Symes to beat the outside chasers to the line and sprint back to the posts for 20-19 with eight minutes left.
Refusing to panic, Pirates kept the ball in tight as prop Willie Kabakaba led his team forward, locking possession down on their own side of halfway as the clock began to tick down.
Pirates coach Phillip Morris admitted later he thought the better option was a long kick to a corner lineout, and it nearly proved prophetic as referee Gordon Ririnui caught Pirates overextending and blew the whistle.
With all eyes on Bobo Ulukuta, his kick looked for all money like it was on line, until it began to drop and bent outside the posts at the last moment.
Having achieved the impressive feat of winning back-to-back Premierships with two different clubs, Morris acknowledged the difference had been Pirates' big match experience.
He had been worried at Tuesday night training the team did not have their usual intensity, but veterans Tyrell and Lasa Ulukuta stamped that out by Thursday.
"I thought our short game was very intelligent," Morris said.
"I asked them to use their brains, sometimes this year they haven't. It was worthy of a final, we knew Border would come back.
"I'm just so proud of the group, they worked hard through that [June] flood, with no [Spriggens Park] training. They're just a hardcore group."
Border coach Ross Williams knew his team had left their run too late.
"We didn't have enough of the ball in the first half. We had it once in 15 minutes and we kicked it away. You can't win a football game with that."
"Really proud of the way we came back. But congrats to Pirates, they got the spoils on the day."
-Integrity Motors Pirates 20 (Denning Tyrell, Lasa Ulukuta tries; Tyrell 2 pen, 2 con) Waverley Harvesting Border 19 (Renato Tikoilosomone, Poasa Waqanibau, Tom Symes tries; Bobo Ulukuta 2 con). HT: 13-0.