The Jamaican sprint star withdrew from the team trials on Friday, having run a time of 10.04 seconds in the semi-finals earlier in the day.
Bolt, 29, is a six-time Olympic gold medallist, two-time defending champion in the 100 metres and the world record holder.
He revealed he had torn his hamstring, setting his sights on the London Anniversary Games on July 22.
"After feeling discomfort in my hamstring after the first round last night and then again in the semi-final tonight I was examined by the chief doctor of the national championships and diagnosed with a grade one tear," Bolt wrote on Twitter.
"I have submitted a medical exemption to be excused from the 100m final and the remainder of the national championships.
"I will seek treatment immediately and hope to show fitness at the London Anniversary Games on July 22 to earn selection for the Olympic Games in Rio."
The injury is a huge blow to Bolt with the 100 metres at the Olympics scheduled for August 13-14.