Bojan spared Stoke's blushes by equalising in the 86th minute after George Miller's 68th-minute opener before the Potters won 4-3 on penalties.
However, the result sees the Staffordshire club sitting at the bottom of the Northern Group C table which is not enough for them to advance to the next phase of the cup.
Former Barcelona forward Bojan scored for Mark Hughes' senior side in the weekend's 1-1 draw with West Ham United but wanted to do everything he could to help the U23 team, such is his passion for the game.
Football is my passion.
Football is my life. pic.twitter.com/ddNyFSU4tm
— Bojan Krkic (@BoKrkic) November 8, 2016