Procter and Pepper went in heat one, with Procter leading from the front.
Pepper came back hard though, and just pipped his teammate to the wall in 2:01.27.
In the second heat Rodgie finished third in a time of 2:03.63 to qualify eighth-fastest for the final.
Australian Daniel Fox set a new Paralympic record of 2:00.11 in heat three, almost becoming the first man to go under two minutes.
The final takes place at 5.48pm this evening.