Phelps, who finished a close second to Ryan Lochte in Thursday's 100 metres butterfly in his first race in two years, used his Friday heat in the 50m freestyle to practice his butterfly stroke.
Although he was entered in a specialist freestyle sprint event he has never swam at a major meet, he opted to change strokes and swim butterfly, which is allowed under the rules of freestyle swimming.
Phelps touched the wall in 24.06 seconds, slightly quicker than he finished his first lap the previous night, but way off the pace of the competitors who swam traditional front crawl.
He finished seventh in his heat and 42nd overall, missing a spot in Friday's final or consolation, and bringing to an end his first meet back.
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Although he was beaten in the 100m butterfly final, one of three events where he still holds the world record, Phelps said he was satisfied with his comeback.
He had been in a race against time to lose some of the weight he piled on since quitting after the 2012 London Olympics with a staggering career total of 18 gold medals.
As expected, his times over the past two days were below his peak performances but still safely under the qualifying standard for the U.S. national championships in August, which double as the selection event for next year's world titles in Russia.
"I was just kind of literally getting my feet wet again," he said.
"This is one meet, it's one race. It's a long way from whether I decide to continue or not, but this was awesome.
"I'm really excited about how things went and I do know what I need to do if I want to continue and want to swim faster and obviously I like swimming faster and faster every race."
While Phelps has still not committed himself to the 2016 Rio Olympics in 2016, there were plenty of encouraging signs that he is anything but a spent force.
"I was very pleased," his longtime coach Bob Bowman said. "His times and his stroke was good, I liked that."
(Editing by Gene Cherry)
