Thompson, who won the 100 on Friday, was passed by Shelly-Ann Fraser-Pryce in the first 50 metres but surged home to regain the half-lap title she last won in 2015.
Fraser-Pryce, beaten by Thompson in a photo finish in the 100, was once again second best, clocking 22.22 ahead of Schillonie Calvert (22.92).
Thompson said it had been a tough four days at the trials.
"Now that the championship is over I finally can sleep and eat some good food, go back to the drawing board, I have Prefontaine Sunday coming so I have to just regain my focus," she told Reuters.
She also confirmed her intention to compete in both the 100 and 200 at the Sept. 28-Oct. 6 world championships in Doha.
In the men's 200, Rasheed Dwyer came home in 20.23 to deny Yohan Blake (20.27) the sprint double with Andre Ewers third (20.48).
Shericka Jackson produced a lifetime best of 49.78 to win her second 400 title and said the time, the second best of the year behind Olympic champion Shaunae Miller-Uibo (49.05), sets her up well for the rest of the season.
"I've been really working hard, 2018 was my off year to get some speed in and I think it has worked pretty well along with the strength and conditioning work and it's really good to know I just ran a life time best here," Jackson told Reuters.
World champion Danielle Williams was disqualified from the 100 hurdles and three athletes sustained injuries, leading to the national athletics association voiding the race.
The men's hurdles was won by Commonwealth Games champion Ronald Levy (13.23) ahead of world under-20 silver medallist Orlando Bennett (13.27) and Andrew Riley (13.33).
In the field, Shanieka Ricketts retained her triple jump crown (14.73) ahead of Kimberly Williams (14.39) while O'Dayne Richards, bronze medallist from the 2015 world championships, won the men's shot put (19.93).
(Editing by Peter Rutherford)
