The 26-year-old from Teesside won the race in 6.50 seconds, ahead of fellow Briton Theo Etienne, who clocked a personal best of 6.56.
Only Jamaica's Asafa Powell (6.49secs) has run faster than Kilty in 2016.
Kilty will not defend his World Indoor title this month in order to focus on preparations for the Olympics.
Andrew Robertson has been handed the second 60m spot alongside James Dasaolu, after he recorded a lifetime best 6.54s at the British trials last week.
The 25-year-old from Manchester was picked ahead of Sean Safo-Antwi.