It was Whetstone who forged ahead 10 minutes before the break when their right-winger played a lofted diagonal ball into the Lions area, which caught out Alex Randall and Aidan Raphael and allowed their striker to fire past Jack Rifkin.
Lions failed to produce anything for the remainder of the half and half-time couldn't come soon enough. The Lions made several changes at the interval, with Sam Hamerton replacing Max Misrahi, allowing the lively Jack Mattey to move inside to central midfield.
The reshuffle resulted in the Lions looking more of a threat at the start of the second half. Both teams struggled to created openings, with Lions's centre-back pairing of Nathan Anders and Raphael in commanding form.
As the second half progressed, the Lions started to push Whetstone back and a tactical reshuffle changed the game. Ethan Novak was thrown further forward down the left, with the ever-reliable Ben Feldman coming in at left-back. Ben Lazarus was introduced at right-back which enabled the energetic Hamerton to drive the team on.
The Lions equalised with 15 minutes remaining when the industrious Hamerton drove at the Whetstone back-line which caused panic in the area. The ball feel kindly to captain Green who beat a player and from a tight angle shot across the keeper into the bottom left corner.
With their tails up, the Lions continued to press and win the ball high up the pitch. The midfield of Novak, Green, Hamerton, Misrahi and Mattey were in the ascendency, with Alex Rose and Nathan Davis chasing everything down.
The pressure finally told with three minutes remaining as Green found himself in the right place at the right time and scored from a similar angle as his first.
The impressive Randall came back on to replace Mattey who had run himself into the ground. Whetstone threw everything forward but the Lions back five of Rifkin, Feldman, Anders, Raphael and Lazarus stood firm before the final whistle sparked scenes of wild celebration.
Lions manager Mark Rose: "This was a case of third time lucky for the boys. We had lost our two previous cup finals and today made up for those defeats. It wasn't pretty, but hte main aim in a cup final is to lift the trophy at the end of the game and that's what we did.
"I just want to mention my co-manager Darryl Lazarus who was missed the game today due to a very important business trip ... in Vegas! He has been top-class all season and this win was for him."
Lions coach Darren Yarlett said: "I'm so proud of the lads. I've only been with them since September and their attitude and willingness to learn has been first class - they now have an identity and a structure in the way the club wants them to play and have taken all this on board which is a credit to themselves.
"This group will only get better and better. Everything is there for them to improve with the facilities and coaching at their disposal.
"In my opinion this is the future of Jewish football. They will get all my time and effort to reach the end goal for Lions and hopefully for future GB squads at European and World Games.
"A huge amount of credit has to go to Mark and Daryll who ended the season off with a second place finish and as cup winners.
Speaking about the departure of skipper Green, Yarlett said: "It's a real shame for the club, but Jordan has decided to join his Brent district side who will enter Sunday morning football from next season.
"For me personally I can only encourage him to go and play the highest standard possible and experience something else and he knows the door is always open at Lions if he wishes to return.
"With my involvement now confirmed back with the Saturday 1st team, some of the players will be invited to train with senior members of the club throughout the season and Jordan would have been a part that to help his development.
"With my link between the U16's and 1st team opportunities will always be given to the best players and hopefully one day he will return."
