As the half wore on Brady started to take control, and nearly scored from a Ben Joseph free kick that eluded everyone but was turned round the post by the alert Josh Samberg in the Maccabi goal.
The second half started as the first finished and Brady should have scored from a corner when Josh Gordon missed from inside the six-yard box.
Shortly afterwards Manchester lost Oliver Gilbert to a straight red for an over-the-top tackle and Brady took advantage straight away when Ellis powered in a great header from a Brad Sharp corner.
Despite being down to 10 men, Manchester came back into the game but the central defender pairings of Jordan Nathan, Jonny Ellis before he went off injured and Ryan Fox stood firm and Brady held out for a great win.
Jubilant Brady boss Joel Nathan told JC Sport: "The game was not the greatest advert for football, but we knew we were in for a battle and when it got tough they couldn't deal with our stronger players.
"We now have a semi-final to look forward to and hope to go one stage further than last season."
