London Olympic champion Nathan Adrian dominated a race featuring seven Olympians to win in 48.31 seconds, while Ryan Lochte, swimming in lane eight, finished second as Phelps touched in 49.17.
It was the most significant race for Phelps since he came out of retirement in May, nearly two years after winning his record 18th Olympic gold medal.
His seventh-placed finish ensured he did not qualify for the event at the Pan Pacific Championships to be held on the Gold Coast in Australia later this month, though he still has the 100 butterfly, 100 backstroke and 200 individual medley to swim in order to qualify for the U.S. team.
Adrian described his swim as 'not great' but was nonetheless pleased to win.
"The third 25 I took off a little bit and then held on at the end," he told USA Swimming's website "It's an extraordinary field and it's an honour to be part of it."
Lochte, swimming in lane eight, was satisfied with the runner-up spot as he works his way back from a serious knee injury he suffered in November.
"This year has been the biggest rollercoaster of my life," the 30-year-old said. "I couldn't see the rest of the field. I just had to put my head down and hope for the best."
In the women's 100 freestyle, 19-year-old Missy Franklin mowed down fellow teenager Simone Manuel with almost the final stroke to claim a narrow victory in 53.43, matching her own championships record.
"I knew I was going to have to come home so fast," Franklin said.
In the men's 200 butterfly, Californian Tom Shields swam a personal best as he built a big lead after 100 metres and held on for an emphatic victory by nearly a second in 1:55.09, the third fastest in the world this year.
(Reporting By Andrew Both in Cary, North Carolina; Editing by Greg Stutchbury)
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