Kermorgant, whose late equaliser at The Valley last week earned the Addicks a replay after they had trailed 2-0, struck his first in the 35th minute with a fine drive.
Simon Church laid the ball off to him 20 yards out and his sweet left-footed shot was too powerful for goalkeeper Ryan Clarke, who could only divert the ball high into the net.
Oxford, unbeaten away in the league this season but with indifferent form at home, were still trying to recover from that goal when Chris Powell's team struck again on their next attack in the 38th minute.
Church raced forward following a slip by Michael Raynes and, after drawing Clarke, he squared it for Danny Green to knock in from three yards.
Oxford played with more urgency at the start of the second half and Josh Ruffels went close to pulling one back with a header.
But Kermorgant sealed Charlton's first win of 2014 with a brilliant 25-yard free-kick curled into the top corner on 58 minutes.