After finishing fifth in the women's long jump final, Jones ran the second leg for the United States 4x100 relay team who had expressed confidence before the race that they could break the world record set by East Germany in 1985.
But despite screaming "Wait, wait, stop" to the third runner on the team as she completed the second leg, Jones could not reach Lauryn Williams with the baton.
When she finally made contact on the fourth attempt it was all far too late for the Americans and Williams did not even attempt to catch up to the runners flying away in front of her.
Jamaica went on to win the gold ahead of Russia and France.
Jones, who won three gold medals and two bronzes at the 2000 Sydney Olympics, qualified only for the long jump in the individual events at the Athens Games.
She has also been investigated by the U.S. Anti-Doping Agency after the BALCO laboratory in California was raided following the discovery of the designer steroid THG (tetrahydrogestrinone).
In addition her partner Tim Montgomery, the world 100 metres record holder, has received a letter from USADA alleging serious doping allegations.
EXTREMELY DISAPPOINTING
"I exceeded my wildest dreams in a negative sense," Jones said. "We were looking for great things to happen, they didn't happen today."
"It's extremely disappointing, words can't put it into perspective."
Tatyana Lebedeva led a Russian medals sweep in the long jump after taking a bronze in the triple jump.
Lebedeva, who cried after finishing third on Monday, leaped 7.07 metres in the second round.
Compatriots Irina Simagina and Tatyana Kotova took silver and bronze respectively. Both jumped 7.05 with Simagina getting second place on the countback.
Liu Xiang equalled the world 110 metres hurdles record when he streaked to victory in 12.91 seconds, becoming the first Chinese man to win an Olympic track and field title.
The new Olympic champion equalled the mark set by Briton Colin Jackson 11 years ago at the Stuttgart world championships.
Liu shot out of the blocks after the field had been given a false start and skimmed over the 10 flights to beat American Terrence Trammell, the 2000 Sydney Olympics silver medallist, into second place just ahead of Cuba's Sydney champion Anier Garcia.
Chinese Xing Huina beat the Ethiopians at their own game to win the women's 10,000 in one of the biggest upsets of the athletics programme.
Xing surged with 100 metres to go to clock 30 minutes 24.36 seconds. Ethiopians took the next three places with silver going to Ejegayehu Dibaba and the bronze to twice-Olympic champion Derartu Tulu.
Tim Mack won the men's pole vault with an Olympic record 5.95 metres ahead of American teammate Toby Stevenson. He then failed with three attempts to extend the record to six metres, which would have equalled Stevenson's season's best.
World record holder Osleidys Menendez of Cuba predictably won the women's javelin gold, launching her first throw 71.53 metres.
The mark was nearly three metres longer than Trine Hattestad's 2000 Olympic record, one centimetre short of the Cuban's own three-year-old world record and four metres better than the lifetime best of anyone else in the final.
