Phelps, who only just reached the medley final by clocking the seventh best time in the heats, has chosen not to compete in the high-tech bodysuit which will be banned from January 1.
Prior to that date, swimmers are free to race in the bodysuits that produced a frenzy of world records at the world championships in Rome in July.
All swimmers in the final wore bodysuits except Phelps, who was taking part in his first short course event since 2006.
"It's been a while and it's a lot different to racing long courses," said Phelps. "There's a ton of walls, and in the one hundred you have to have good walls.
"I tried to hit every wall, but I know I didn't hit my first wall right, so I'm kind of disappointed but happy overall."
Phelps is entered for another two races on Wednesday in Stockholm, after which he will compete in Berlin at the weekend.
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