Merritt, 30, the reigning Olympic champion and world record holder, was edged into fourth place in a photo-finish at Hayward Field.
Devon Allen won the event in 13.03 seconds from Ronnie Ash in second and Jeff Porter in third.
Porter took third in 13.206 with Merritt just a fraction behind in 13.22.
It was the end of a remarkable comeback from Merritt, who underwent a kidney transplant in September last year just days after competing at the World Championships in Beijing where he claimed a bronze medal.