Felix, the three-time world 200 metres champion, won Olympic gold at the 2012 London Games in the 200m, the 4x400m relay and the 4x100m relay.
A four-time Owens Award winner, the 26-year-old also became the fourth fastest woman ever when she clocked 21.69 in the 200m at the US Olympic trials in Eugene, Oregon.
"I am honoured to have the Jesse Owens Award again and it truly is a dream come true for me," Felix said on a conference call. "I have been blessed with good health over the years and have been able to take advantage of that.
"What made this year so special is the journey that I have been on my entire career. From having (won Olympic) silver medals in 2004 and 2008, I feel like that really motivated me."
Eaton produced sensational form in 2012, setting world records in the heptathlon at the world indoor championships and also in the decathlon at the US Olympic trials.
In rain-soaked conditions in Eugene, he became only the second decathlete to break the 9,000-point barrier as he eclipsed the previous mark set by Roman Sebrle with a haul of 9,039 points.
Eaton, 24, went on to claim Olympic gold in London with a performance of 8,869 points.
"The Olympic year was my first one and I had a lot of expectations for myself," said Eaton. "It was fun afterward but leading up was stressful. Now I am kind of relaxed and feel like I have accomplished a goal.
"I wanted to see what it felt like to be on the first tier podium at the Olympics. With the Olympics on my mind, it was easy to check off the other goals as I went along."
Felix and Eaton will be presented with their awards on December 1 in conjunction with USATF's annual meeting at Daytona Beach, Florida.
Athletics great Owens won gold medals in the 100 and 200 metres, long jump and 4x100 metres relay at the 1936 Berlin Olympics.