The 18-time Olympic gold medallist finished second to Tom Shields but still booked his place at the Pan Pacific Championships in Australia in late August.
Phelps, fastest in the heats with a time of 51.17seconds, clocked 51.30secs to be just 0.01secs behind Shields.
Having only returned to competitive swimming in May, Phelps said it was an indication of where he was at.
"Once I hit the 16th stroke and was a little long hitting the wall, I knew I was a little off," Phelps said.
"To be honest, this is where I am. With having a year and a half off, I need to put in more work. This is something that motivates me more than anything else.
"I can't stand to lose and this will be something that will stick with me through Pan Pacs, and next year at [the World Championships]."
&format=webp)
-
Other Sports 13.02.2017Nike film for equality
-
Other Sports 22.11.2016Goldberg beats Brock Lesnar in 90 seconds at Survivor Series. -
Other Sports 15.06.2016F1 star turns to an old man in new commercial
-
Other Sports 10.03.2016Tennis star announces she failed a drug test at 2016 Australian Open
-
Other Sports 20.01.2016French tennis star pauses game, attend to girl struck by ball
-
Other Sports 15.12.2015F1 Champ says he played his music for Kanye West
-
Other Sports 26.11.2015Late wrestler's DVD and Blu-ray to premiere December 2
-
Other Sports 24.11.2015UFC Champions calls Floyd Mayweather the 'greatest ever'
-
Other Sports 17.11.2015Veteran artiste Sound Sultan shares on how he became a basketball team owner
&format=webp)
&format=webp)
&format=webp)
&format=webp)
&format=webp)
&format=webp)
&format=webp)