Scott triumphed in a time of 47.90 seconds and booked his place at this summer's World Championships along with Max Litchfield, who also broke a British record to win gold in the 400m individual medley.
Charlotte Atkinson clinched gold in the women's 200m butterfly, adding to the 50m title she won on Wednesday.
Litchfield clinched his spot at the Worlds by finishing in an automatic qualifying time of four minutes 10.63 seconds.
Atkinson, who comes from the Isle of Man, secured a consideration mark of two minutes 7.06secs for the summer championships.
Commonwealth bronze medallist Dan Jervis also achieved a consideration time on the way to an emphatic victory in the 1500m freestyle, finishing in 14 minutes 51.48secs.
The Welsh swimmer, who works as a painter and decorator to fund his training, described the victory as "amazing".
In Thursday's other final, Anna Hopkin won the 50m freestyle in a time of 25.07secs, which was outside of the consideration time.
Duncan Scott became the first British man to swim under 48 seconds in the 100m freestyle as he broke his own national record to win gold at the British Swimming Championships.