Merritt won the Inspiration Award for his season, which included a gold medal and a world record in the 110 hurdles.
Rudisha, who was named Athlete of the Year in 2010, won the Performance of the Year award for his record setting gold medal run in the 800 meters.
Javelin thrower Keshorn Walcott of Trinidad and Bahamas sprinter Anthonique Strachan won the Rising Star awards.
The awards were announced on the final day of the IAAF's 100th anniversary celebration.
