Looking short of her trademark explosive power, Jones clocked 11.14 seconds as the field pulled away in the final third of the race.
Only the top three finishers are guaranteed a place in the team for next month's Games providing they have met the Olympic qualifying standard.
Jones's former team mate LaTasha Colander won the race on Saturday in a personal best of 10.97 seconds. The time equalled the second fastest in the world this season.
World champion Torri Edwards was second in 11.02 seconds and collegiate winner Lauryn Williams took third in 11.10 seconds.
Four years ago, Colander won a gold medal with Jones in the women's 4x400-metre relay at the Sydney Games after winning the individual 400 metres final at the trials.
However, this season she has concentrated on the shorter sprints.
Jones, who has been under scrutiny by the U.S. Anti-Doping Agency although she has never failed a doping test, will now attempt to qualify in the 200 metres and long jump.
At the Sydney Games, she won gold in the 100, 200 and 4x400 metres relay and took bronze in the long jump and 4x100 metres relay.
Jones returned from taking a season off for the birth of her first child and was targeting another multiple gold medal haul at an Olympics.
But her progress has been far from smooth following a string of poor performances in addition to the doping scrutiny.
HURRIED AWAY
Jones left the track without answering any questions from awaiting reporters.
"When I talk, you guys have something negative to say. When I don't talk, you have something negative to say," she said as she hurried away.
"I'd rather not talk and spend the time with my son."
Jones's boyfriend and the father of her son, world 100 metres record holder Tim Montgomery, and Olympic champion Maurice Greene were among those making it through the first two rounds of the men's 100 metres.
Greene won his quarter-final in 10.06 seconds.
Montgomery, who faces a lifetime ban after being charged with a doping offence by the USADA, qualified fourth in a later race at 10.16 seconds.
World 200 metres champion John Capel and Shawn Crawford ran even faster than Greene. Capel clocked 10.01 seconds to win the second quarter-final and Crawford took the third race in 10.00 seconds.
The semi-finals and final will be raced on Sunday.
SHOT SHOCK
In other events, Olympic silver medallist Adam Nelson claimed the men's shot put title with a heave of 21.64 metres but world indoor champion Christian Cantwell failed to make the team.
Cantwell, who had the four best throws in the world this year, fouled five times and wound up fourth with a best of 20.51 metres.
Reese Hoffa took second at 21.14 metres and three times world champion John Godina was third at 21.08 metres.
Chryste Gaines, who like Montgomery has been charged with a doping offence by the USADA without a positive test, did not advance past the women's 100 metres semi-finals.
Former world 200 metres champion Inger Miller was also eliminated in the 100 metres semi-final.
World 400 metres hurdles silver medallist Joey Woody also failed to advance.
He finished fifth in his semi-final in 49.19 seconds as rising star Bershawn Jackson produced the fastest time of the day at 48.28 seconds.
The trials continue through July 18.
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