The Championship side looked set to exit the competition when they went two goals down in the initial tie last week, but Oxford, who sit seventh in League Two, were ultimately pegged back.
Kermorgant was the man to force a replay with Charlton's equaliser at The Valley and the Frenchman was the scourge of Oxford again on Tuesday with goals in either half.
His first came after 35 minutes courtesy of a driven effort from the edge of the area.
Danny Green left Oxford with a mountain to climb just three minutes later, prodding home from close range after Simon Church had nodded across goal.
Oxford were unable to mount a fightback as Charlton had done a week earlier and fell further behind when Kermorgant found the net again with a 30-yard free-kick.
Chris Powell's men face a trip to fellow second-tier outfit Huddersfield Town in round four on Saturday.
