The performance was part of the late night show's Classroom Instruments segment that involves guests and The Roots using items such as hand clappers, a kazoo, an orange shaker and a triangle to recreate the song.
Cabello, and the rest of The Tonight Show crew, were all seen wearing tropical themed attired complete with sunglasses.
Fallon during the performance used different instruments throughout as he switched between a wood block, bass drum and a Casio keyboard.
"Havana" was released as part of Cabello's solo debut album, Camila . The album is Cabello's first since departing music group Fifth Harmony.