The 30-year-old, excluded from the World Championships by USA Swimming after a drink-drive conviction, won in one minute 54.75 seconds in Texas.
Phelps, an 18-time Olympic champion, also recorded the year's fastest times to win the 100m and 200m butterfly.
Ryan Lochte won world 200m individual medley gold in 1:55.81 on Thursday.
American Lochte, 31, also holds the world record for the event of 1:54.00, which he swam in 2011.
"Ryan and I have been pretty dominant in that race since we started racing back in 2004," said Phelps.
"I'm looking forward to getting back in and competing with him.
"I've been away from the sport for a while and I feel like I'm kind of back where I used to be. It's good to be here."
On Saturday, Phelps won the 100m butterfly in 50.45 seconds, faster than the 50.56 South African Chad Le Clos swam to win world gold on the same day.
A day earlier, Phelps won the American 200m butterfly title in one minute 52.94 seconds in San Antonio - 0.54secs faster than Hungary's Laszlo Cseh swam in winning the world title in Kazan, Russia.
Phelps, who was convicted of drink-driving in December and served a six-month ban from competition, now has a record 55 national titles.

Toilet roll, chocolate biscuits, orange juice and antibacterial wipes were all on the list of shrinking items reported by Which?.
The consumer group argued that making products smaller was a "sneaky way" of increasing prices.
It is further evidence of a trend towards shrinking products.
In January Unilever revealed that a number of ice creams it makes would be getting smaller.
The latest list from Which? includes:
Most brands, responding to the Which? research, said it was up to supermarkets to set the price. However, they would not disclose if they had charged the stores a lower wholesale price.
"Shrinking products can be a sneaky way of increasing prices. We want manufacturers and supermarkets to be upfront about shrinking products so consumers are not misled," said Which? editor Richard Headland.

Natalia Wilkanowska, 50, disappeared in 2003 after travelling to visit her ex-husband Gerald Doherty in Luton.
Her body was found in December 2015, Luton Crown Court was told.
Mr Doherty's brothers, Joseph and Daniel, are on trial accused of helping conceal her remains and lying to police.
The court heard Natalia was last seen by her children in April 2003 when she left her Eastbourne home to travel to Luton.
Prosecutor Neil King said her ex-husband was responsible for her death. The couple had separated in 2001 after 23 years of marriage.
Mr Doherty took his own life at a flat in Port Glasgow, Renfrewshire, on their wedding anniversary in July 2003. He had been receiving psychiatric care.
His two brothers, who both wore hearing loops in the dock, face a total of seven charges.
Natalia's death came to light in 2014 when Joseph Doherty revealed Gerald had murdered her, but that her remains had been "chopped up".
Mr King told the court Natalia's body was found a year later - intact - under rubble in the garden of Daniel Doherty's house in Icknield Way, Luton.
She had suffered "a blunt force trauma" inflicted by a third party, but the cause of death could not be established.
Read more on this and other Bedfordshire stories
Mr King said Daniel Doherty, who worked as a builder, must have "connived in the deposition of the body".
He said both men lied to the police and obstructed the coroner.
Daniel Doherty, 67, of Icknield Way, Luton denies two charges of perverting the course of justice and two charges of obstructing the coroner, by aiding and abetting the concealment of a body and lying to police.
Joseph Doherty, 73, of Old Greenock Road, Port Glasgow, denies perverting the course of justice and obstructing the coroner by giving a false account of her death.
Both men also deny preventing lawful burial.
The trial continues.
Olympic great Michael Phelps swam a third 2015 world-best time in as many days in the 200m individual medley at the USA National Championships.
[NEXT_CONCEPT]
A consumer group has revealed its latest list of shrinking supermarket items that still cost the same, or more.
[NEXT_CONCEPT]
A woman's body lay under builders' rubble in a back garden for more than 12 years before it was discovered, a jury has heard.