The first and only sword duel between Guinevere and Morgana occurred following Helios's and Isolde's mortal wounding, and the victory of Arthur, Tristan and the knights of Camelot over the Southrons. Guinevere confronted Morgana in Morgana's Chambers. Morgana had earlier been stripped of her magic with Merlin's enchanted poppet, and had been wounded in the hip by a knight of Camelot, so could only fight one-handed. She was seen walking towards her chambers and was thought to be fleeing, but later returned for an unknown reason and confronted Gwen. Guinevere chose to find one-handed until her final strike, which Morgana used to throw the sword out of her hand and corner her. Morgana also fought with one-handed since she was fatally injured. Just as Morgana was about to strike Guinevere in the throat to finish her off, Merlin used a stunning spell on Morgana through the doorway, but was not seen by Guinevere, and likely Morgana. As Morgana hit the ground a few meters back, she vanished into thin air.
How this happened is unknown, whether it was her own magic, Merlin's, someone else, or another force (The Sword in the Stone).
Victory: Merlin
Transcript
An exchange of words took place during the duel:
GWEN
What did I do to make you hate me so much?
MORGANA
It's not what you did, it's what you're destined to do! I'm sorry, Gwen, but I can never let that happen!
--After Morgana's defeat--
MERLIN
Are you alright?
GWEN
Yes.
What happened?
MERLIN
...I don't know.
(The Sword in the Stone (transcript))