South were up against it after keeper Akiva Lieberman was forced off with an ankle injury after 30 minutes.
Brady started the second half on the front foot and the match came to life around the 50th minute when South Manchester's Harvey Kaye was sent off following his second cautionabl offence.
Brady took advantage within 10 minutes when Ben Joseph was brought down in the area and up stepped captain marvel Ellis to slot home the penalty.
South didn't panic and tried to play some nice football, but ultimately they were unable to break Brady down.
The fans were then treated to a piece of magic that would've graced any cup final. Man-of-the-match Josh Gordon produced an excellent last-ditch challenge on the edge of his area and Hershman collected the ball in his own half on the left wing and went on a run that saw him cut inside before unleashing an unstoppable right foot shot in the the far right hand corner from 30 yards.
With man-of-the-match Josh Gordon pulling the strings in midfield, there was no way back now for South's 10 men and Brady's celebrations began in earnest when Hershman saw his shot tipped on to the crossbar, allowing the alert Green to tap home.
Brady joint-manager Josh Rosenfeld told JC Sport: "The win tops off how far we have come this season. We deserved to win the cup as we have been on a run since before Xmas where at times we are unplayable.
"The hard work, effort every individual in the squad has put in over recent months, the boys deserved their special day and have the right to call themselves all champions.
"If you look at our cup run we smashed Lions, Redbridge and two hard away days in Manchester. The boys are fantastic, the squad are close and everyone of them play for each other.
"Everyone today did Brady proud and it's an honour to be the first ever Brady side to win the Morrison. The game today started off tight. Both sides had the play with only us causing a real threat. We knew going in half time we were the stronger side and had the belief to go and win the game. We had a small bit of luck with their keeper getting injured and they went down to 10, but was fully deserved two yellow cards. We out played them in the second half and ran out comfortable winners. What a weekend and what a day for everyone involved at Brady."
Co-manager Joel Nathan told JC Sport: "Yes things went our way with their keeper going off injured and the sending off, but we came up here with a game-plan and the boys executed it to perfection.
"Our keeper didn't have a save to make and for me even when the score was level we never looked like losing.
"I have either played or managed the club for 33 years and this has to be my greatest club moment, especially as my son was playing.
"Special mention has to go Josh Rosenfeld as without him this team would not be together. We now have three matches left in the season and are still in with a chance of finishing second and that is what we will be aiming for as we will not rest on our laurels."
South Manchester boss Loz Newman told JC Sport: "Firstly, congratulations to Brady on winning the National Cup - a fine achievement from Joel and his boys and well deserved.
"It was an even first half and the game changed on two moments. Losing our keeper to injury in the first period meaning we ended up putting our top-scorer Adam Lavin in goals mainly due to his height to combat Brady’s excellent deliveries. Then losing Harvey Kaye to a red card on 48 minutes. If felt like everything that could go wrong went wrong for us, but that said we created few chances and weren’t really at our best.
"Brady worked hard and in the end the extra man paid off for them. I am sure they may feel they could have had penalty in the first half, but am also sure they know it could have been very different had we stayed 11 versus 11 and had our goal keeper.
"I actually ended up playing the last half an hour in goal as we took Adam out to try and salvage the game and found out we won the league from the sidelines (as Miam Miam lost their penultimate game) with a few moments to go. At that time it didn’t help the disappointment, but on reflection now it’s a fantastic achievement for the Club to have retained a non-Jewish League for the first time ever.
"We had great support on Sunday and I want to thank them all for coming down. It was a great occasion and whilst many of this current side now move on to pastures new we hope to be back next year."
