Bundesliga champions Bayern were denied a domestic double after Niko Kovac's Frankfurt claimed a controversial 3-1 win in Berlin on Saturday.
Ante Rebic scored a brace, netting in the first half and again on the counter-attack with eight minutes remaining after Robert Lewandowski had equalised for Bayern.
VAR had ruled in favour of Rebic for Frankfurt's second goal in the 82nd minute following calls for handball and Kovac's men were fortunate again when referee Felix Zwayer turned down penalty appeals from Bayern players in the fourth minute of stoppage time, with Boateng appearing to foul Martinez in a frantic finish.
Mijat Gacinovic then sealed Frankfurt's fifth cup trophy on the break and Boateng admitted he was fortunate not to be penalised prior to that tournament clinching strike.
"I met him clearly, then the referee must decide," Boateng said. "Honestly, I thought that he was going to award a penalty.
Pokalsieger pic.twitter.com/7QHGM8EdPQ— Kevin-Prince Boateng (@KPBofficial) May 19, 2018
"But we have been lucky that he did not give a penalty. He has to whistle, I'm always honest, that's why I have to say so."
Serbian midfielder Gacinovic added: "I am glad that I have finally scored a goal - and such an important one, too."