The duel between Guinevere and Morgana occurred during Arthur's Second Rebellion of Camelot.
Events
After Morgana discovered that her magic was being blocked, she fled from the throne room and Gwen and Merlin chased after her. Gwen eventually caught up with her in a corridor and they began to duel.
Though Morgana had been wounded in the side and could only fight one-handed, she easily gained the upper hand. She disarmed Gwen and prepared to kill her with a strike to her throat, but Merlin blasted her away from Gwen with a powerful stunning spell.
Morgana was thrown backwards through the air and parts of the ceiling collapsed around her. When the dust cleared, Gwen and Merlin discovered that she had vanished (The Sword in the Stone).