Bnei Yehuda held their nerve to win a penalty shoot-out at the Teddy Stadium in Jerusalem.
After a dour, goalless 120 minutes, Bnei Yehuda won the resultant shoot-out 4-3, with former Premier League stars Yossi Benayoun and Tal Ben Haim missing spot kicks for Maccabi.
This was Bnei Yehuda's third FA Cup with the team from Tel Aviv's Hatikva quarter previously winning the trophy in 1968 and 1981.
"It's still d to believe that the cup is ours," said Bnei Yehuda captain Yitzhak Azuz.
"We've finally brought a trophy to this club that everybody loves so much. The fans really deserve it and let's hope that this will be the first of money more trophies."
Maccabi Tel Aviv will also play in the Europa League qualifying rounds as Ligat Ha'Al runners up as well as third placed Beitar Jerusalem.
Champions Hapoel Beer Sheva will play in the Champions League.