Jonas hit the post and Mattia Perin saved from Joao Felix to allow Alex Sandro to roll in the winning spot-kick, earning Juve a 4-2 triumph after a 1-1 draw at the Red Bull Arena on Saturday.
But Ferreyra leaving the field on a stretcher wearing a neck brace remained the defining moment of a low-key ICC contest that was lit up by two fantastic second-half finishes.
Benfica's new signing Ferreyra caught team-mate Jardel in a heavy collision that left the former Shakhtar Donetsk striker needing lengthy treatment and he will be a serious doubt for next month's Champions League third qualifying round tie against Fenerbahce.
Serie A champions Juve lacked coherence in their play throughout and Benfica took a deserved lead in the 65th minute, Alex Grimaldo deceiving substitute goalkeeper Perin with a 25-yard free-kick that dramatically dipped under the woodwork.
Juve were without big names including star signing Cristiano Ronaldo and Argentina attackers Paulo Dybala and Gonzalo Higuain, and it was Luca Clemenza who produced a superb equaliser with just six minutes to play.
Ferreyra should have tested Wojciech Szczesny more seriously in the ninth minute when he latched on to a long pass, while Claudio Marchisio fired over a low Joao Cancelo cross at the other end.
Mattia Caldara started for Juve despite reports he could join AC Milan in a deal involving a return for Leonardo Bonucci and his mistake handed Gedson Fernandes a fantastic chance, but the midfielder dragged his shot wide.
A long delay for the concerning injury suffered by Ferreyra lowered a sluggish tempo further, the striker carried off on a stretcher after an accidental collision with Jardel in the Benfica box.
Cancelo switched to the left flank at the break and the former Benfica defender almost opened the scoring in the 48th minute, his whipped right-footed curler narrowly clearing the crossbar.
Andrea Favilli struck both goals in a 2-0 defeat of Bayern Munich but the forward was denied by goalkeeper Odisseas Vlachodimos at his near post as Juventus moved through the gears.
But it was Benfica who nudged ahead with a goal of the highest quality from Grimaldo midway through the second period.
Replacement goalkeeper Perin was left motionless by Grimaldo's whipped hit, which looked certain to rise over the top before the ball somehow dropped under the crossbar.
Medhi Benatia should have headed home Clemenza's cross to level the scores in the 76th minute but the centre-back somehow failed to direct the ball home from just a few yards out.
But Clemenza took matters into his own hands with a brilliant late equaliser, the young substitute dancing through a series of challenges before thundering an unstoppable drive home.
Vlachodimos pushed away Alex Sandro's header to force the game to penalties, with Jonas hitting the post with his effort to hand Juventus the advantage.
Perin saved with his legs to keep out Felix's strike and Alex Sandro consigned Benfica to defeat after their ICC penalty shoot-out victory against Borussia Dortmund last time out.
But Benfica coach Rui Vitoria will be more concerned about Ferreyra, with Fernandes also limping off in the closing stages.