Farah admitted after last Saturday's 10,00m victory that his quest for a double World Championship gold would be "tough" - and it showed as the 34-year-old struggled to assert his authority on tonight's race.
The 27-year-old clocked 13 minute 35.69 second, almost one second better than his earlier personal best of 13:36.62, in the first round heat number one but he ended up at the 15th spot in a top class field, which included defending champion Mo Farah of Great Britain, to bow out of the championships.
Farah was less than a second back in 13:33.22, the Kenyan-born America Paul Chelimo winning bronze in 13:33.30.
Britain's track knight had to settle for the silver in the 5,000m as he was denied an 11th successive gold at world or Olympic level in the final championship race of his glorious career.
"Tactically, they worked as a team", said Farah.
"I have to focus on myself".
Farah did well to recover to take second placeSRDJAN SUKI EPA
"To be honest with you it takes so much out of me". Perhaps this was a step too far into greatness, even for an athlete like Farah. I would have loved to have seen Usain win but at this level no-one is going to give it you, no matter who you are. It's not an excuse, but it took a lot more out of me than I realised.
Farah - who immediately went to his family as he has made a habit of doing - said he had had an extraordinary ride in the past six years.
It is also about Kenya's bid to end 12-year gold drought in men's 5,000m, which Benjamin Kipkoech Limo last won in Helsinki, Finland, in 2005.
Govindan Lakshmanan ran his personal best but it was still not enough for him to qualify for the final round of the men's 5000m race in the World Athletics Championships.
Johnson-Thompson tried to tap into the wave of emotion for Farah making her final attempt after the 5,000 race had started, but despite her efforts could not clear the bar.