Phelps’s time, the second-fastest ever recorded in a standard swimsuit, bettered the 50.
56 South African Chad Le Clos clocked to win the same event at the world championships in Russia only hours earlier.
Fellow American Ian Crocker swam 50.40 in 2005, before the introduction of high-tech swimsuits, which were subsequently banned in 2010 after times improved so dramatically they made it impossible to compare eras.
Le Clos, after his victory, trash-talked Phelps, who declined to get involved in a slanging match when asked about the comments in a poolside interview.
“I saw the comments. There are a lot of things I could say but I won’t,” the 30-year-old American said after his triumph.
“I let what I do in the pool do all my talking and that’s how I’ve always done things.”
Earlier, Le Clos had downplayed the significance of Phelps’s Friday victory in the 200m butterfly.
“Phelps did a great time … but with all due respect, that’s not so hard to do when you’re swimming on your own,” Le Clos told reporters.
Phelps is competing in San Antonio rather than Kazan because he was banned from the U.S. team after his drink driving arrest.
But the 18-times Olympic gold medal winner has sworn off alcohol until after next year’s Rio Olympics, and his performances the past two days leave no doubt that he is back.
His winning time in the 200m butterfly was also faster than the gold medal time in the same event in Kazan.
“It goes hand in hand with what I’ve been doing in training. I’m back to actually doing work like I used to and it pays off,” Phelps said.
“It’s not rocket science but you have to work hard. This is a great start for me to go into next year.”
Phelps sounded confident about Rio, but warned the Games were still a long way away.
“A lot can happen in a year, with not only myself but everybody else in the world,” he said. “Hopefully I can keep this going over the span of the next year.”
(Reporting by Andrew Both in Cary, North Carolina; Editing by Larry Fine)