The tournament, which was renamed to honour the Argentine great after he passed away in November, kicked off in October as football returned following a seven-month hiatus due to the novel coronavirus pandemic.
A rock band comprising former professional footballers played live on the pitch before kick off and the stadium was lit up with fireworks and a light show featuring images and quotes from the charismatic former Boca Juniors striker.
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"This cup is a tribute to Diego, and he'll surely be accompanying our celebrations," Boca's Ramon Abila said after the game.
After a tepid first 45 minutes at the San Juan del Bicentenario stadium, Boca took the lead with a spectacular strike from Edwin Cardona 19 minutes into the second half.
Boca, who last recorded a victory on Dec. 27, converted all five of their spot kicks while Jorge Rodriguez missed for Banfield.
Boca's Cup win came after a disappointing midweek defeat to Santos saw them knocked out of the Copa Libertadores, the South American equivalent of the Champions League, at the semifinal stage.