National Championships in Irvine, California on Friday after Tom Shields pipped the 18-times Olympic gold medalist by 0.01 seconds.
Phelps, who came out of retirement in May, touched just after Shields, who clocked 51.29 seconds, but still booked his spot at the Pan Pacific Championships in Queensland, Australia later this month in perhaps his strongest event.
Phelps, who has won the event at the past three Olympics, clocked the fastest time in the world this year at 51.17 in the morning heats but could not replicate the performance in the final.
He was well behind after 50 meters and a mediocre turn left him with a big deficit to make up. It was only in the final few meters that Phelps challenged Shields, who just held on.
Phelps, who retired after the 2012 Olympics, finished seventh in the 100m freestyle on Wednesday, and has two more events over the weekend.
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