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Fraser-Pryce, who took bronze in a fantastic final, became the third athlete in two days to fall short in bid to win three individual athletics titles in a row, after Ethiopian 10,000m runner Tirunesh Dibaba and New Zealand shot-putter Valerie Adams also had to settle for medals of another colour.
Farah will now seek to retain the 5,000m too, hoping to emulate Finn Lasse Viren, the only man to defend both titles in 1976. Every one of Farah's Olympic triumphs have come in virtually the same way as he sits in behind a group of Ethiopians and Kenyans before blasting out an unstoppable final lap.
There was a twist on this occasion, however, as he tripped and fell early in the race when he tangled with his American training partner Galen Rupp with 16 laps remaining.
He bounced up quickly though and with the East Africans failing to test him by pushing the pace, there was an air of inevitability about the outcome as he swept past Kenya's Paul Tanui and roared home.
“It's hard mentally when you go down,” a tearful Farah admitted. “I got emotional because you put so much work in and in one moment it's gone. That one moment could be it.”
The women’s 100m final initially appeared impossible to call after all eight women qualified in sub-11 second times. But as it turned out, Thompson emerged as a comfortable winner in 10.71 after hitting the front at halfway.
America Tori Bowie took silver in 10.83 while Fraser-Pryce, running with a minor injury, edged out Ivory Coast's Marie-Josee Ta Lou by seven thousandths of a second.
“I'm very excited, I'm really happy, Jamaica has so many talented sprinters and to be only the second Olympic champion I'm really happy about that,” Thompson said.
Great Britain’s Jessica Ennis-Hill yielded her heptathlon crown to 21-year-old Belgian student Nafissatou Thiam, who had arrived at the Games hoping merely for a top-eight finish and who delivered a remarkable five personal bests in the seven events. Canada's Brianne Theisen-Eaton claimed bronze after a strong second day.
“I still can't believe it, I didn't come for a medal. I didn't think about it at all,” said Thiam. “It's crazy. I wasn't expecting that - maybe top eight, but not the gold.
"In the 800m I was just trying not to let Jess [Ennis-Hill] go, I thought I could do 2:15 or 16 and not let her go too far. I guess my life is going to change, I am still at university so maybe I have a decision to make.”
Defending champion Ennis-Hill, who returned to Olympic action after having a baby, said she also had a decision to make. "It's so hard to find the words to describe this. It's very emotional,” Ennis-Hill said. “I have to make a big decision about what I'm going to do. This could be my last one,” she said.
The fourth medal event of the night was the men’s long jump. In an edge-of-the seat long jump competition. The USA’s Jeff Henderson continued his country’s proud tradition in the event when he flew 8.38 metres on his final jump, edging out South African Luvo Manyonga. London 2012 champion Greg Rutherford was pushed back into the bronze medal position.
“It feels good to be in that category, to win that many medals,” said the new champion Henderson. “It feels surreal right now.”