The favoured Jones leaped a mere 6.39 metres, making her only the seventh of 12 qualifiers for Thursday's final.
The effort left Jones struggling for a second time in an Olympic trial she had dominated here in 2000.
She finished a shocking fifth in the women's 100 metres final on Saturday and failed to make the U.S. Olympic team for next month's Athens Games in an event she won in Sydney.
Still, Olympic long jump bronze medallist Jones should qualify for the U.S. team on Thursday because only two Americans have made the Olympic qualifying standard of 6.70 metres. Up to three athletes per country may compete in the event in Athens - if they have met the Olympic standard.
She also will compete in the 200 metres at the trials at week's end.
Jones, who is under scrutiny by the U.S. Anti-Doping Agency (USADA) despite never failing a doping test, slipped away from reporters on Monday without commenting on her performance. Her best jump was her first. She then leaped 6.34 and 6.31.
Ola Sesay had the best jump of the competition, 6.63 metres, with Jones's chief rival Grace Upshaw qualifying second in 6.54.
The elimination from the trials of athletes facing doping charges continued with Olympic silver medallist Alvin Harrison bowing out in the men's 400 metres semi-finals.
Harrison, who faces a lifetime ban from USADA in connection with the BALCO doping scandal, finished a non-qualifying seventh in his semi-final.
YOUNG OUT
He said later he and his twin Calvin would file a lawsuit against USA Track & Field. They are alleging the U.S. governing body was prejudiced and biased in allowing Jerome Young to compete in the 2000 Olympic trials when the organisation knew Young had failed a 1999 doping test.
World champion Young was another non-qualifier, fading to fifth in his semi-final.
The Court of Arbitration for Sport (CAS) recently ruled Young should not have been allowed to compete in the 2000 Olympics because of the positive test. He, and perhaps the other members of the U.S. 4x400 metres relay team, may lose their gold medals because of the CAS ruling.
Derrick Brew was the fastest 400 metres qualifier in 44.75 seconds.
World record holder Tim Montgomery and Olympic relay medallist Chryste Gaines had bowed out earlier in the 100 metres. Both face lifetime bans after being charged with doping offences by USADA without a positive test.
Collegiate champion Jonathan Johnson won the men's 800 metres in 1:44.77. Favourite David Krummenacker, the 2003 world indoor champion, never got himself in position to be a factor and wound up fourth.
Three-time Olympian Jearl Miles-Clark, who is 37, claimed the women's 800 metres in 1:59.06 with sister-in-law Hazel Clark third in 2:00.37.
Minutes after the race Clark's boyfriend, Wenston Riley, proposed marriage to her. A nervous Clark said yes.
The trials take a break Tuesday and Wednesday before resuming on Thursday. They continue until July 18.
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