Sci-Twi’s element is also Magic.
In this context, Magic refers to the maintenance of friendship, as per the name of the show. Twilight Sparkle is not the Element of Magic because she’s an excellent unicorn who’s good at casting spells; Star Swirl also fits that description, and was absolutely not a master of the Element of Magic because he is the worst friend imaginable.
Twilight Sparkle bears the Element of Magic because she is the central force that keeps her friend group together. She is consequently the focal point for their giant rainbow lasers which are made out of friendship.
More intuitively, Twilight is the key figure in solving their friendship problems, and eventually teaching the entire world about friendship through a school dedicated to the study.
That is the Magic represented by the element, and Sci-Twi still has it as her Element the same way the others have “Equestrian magic” behind their Equestrian Elements.