Farah continued his unprecedented spell of long-distance domination by landing his eighth straight global crown, but he did it the hard way after falling to the track following a trip from training partner Galen Rupp.
He recovered to respond to the challenge laid down by Kenya’s Paul Tanui, bursting past him down the home straight and crossing the line in 27 minutes 5.17 seconds.
Victory saw him eclipse the Olympic achievements of the likes of athletics double champions Sebastian Coe, Daley Thompson and Kelly Holmes.
But Ennis-Hill fell agonisingly short in her bid to become the first British woman to retain an Olympic title in athletics as she settled for silver, finishing 35 points behind brilliant young Belgian Nafissatou Thiam.
And Rutherford’s run of four straight major championship victories came to an end as a best leap of 8.29m earned him bronze in a thrilling long jump competition.
The trio all won gold in the space of 45 glorious minutes at London 2012, giving British athletics its finest hour. It remains a one-off, for atmosphere and achievement, but three medals in one session was still no mean achievement.
One man, though, remains a cut above.
Farah headed to Brazil on the back of running his fastest 5,000 metres since before the last Olympics and the quickest in the world this year at the London Anniversary Games. It was some parting statement.
“I’m in decent shape”, he had said. He was not lying.
He said he was prepared for an army of Kenyans to try and crush his challenge in Rio. But then they have tried for four years to find his number. And still they cannot succeed.
Farah was content to sit at the back of the field, with the pace slow in the early stages before taking closer order.
Disaster nearly struck when he tumbled to the floor after tangling with Rupp, but he got up, gave his training partner the thumbs up and got right back into the mix.
With 300 metres to go Tanui pressed the accelerator in a bid to neutralise the Briton’s renowned finishing speed, but Farah was not done and powered past the Kenyan before holding on to win by 0.47secs.
He has spoken about the hardship of spending so many months of the year away from his young family pounding out the miles in training. It is victories like these that make that sacrifice worthwhile.
He broke down in tears as he was interviewed by broadcasters after the race. This one mattered.
The father of four said: “When I went down it did take a lot out of me, but I managed to get up quickly. I knew how hard I’ve worked and I wasn’t going to let that go.
“It was hard, mentally. When you go down you’re really emotional.
“It was hard to pick myself up, but I believed in myself and the work I went through. When I crossed the line I got really emotional. I know what goes in and how hard I had to work for it, in one moment it’s gone.
“But I had to believe in myself, I wanted to do it for my kids.”
Ennis-Hill’s scored of 6,775 points was her best since London 2012, but she could not live with Thiam, who produced five personal bests from her seven events.
The Sheffield athlete went into the final event, the 800m, needing to run 9.47 seconds quicker than Thiam to make up a deficit of 142 points.
She produced a hugely gutsy display of front-running to give herself the best possible chance and came home in 2:09.07, but Thiam’s time of 2:16.54 was enough.
Silver, though, was still some achievement two years after the birth of her son Reggie.
Katarina Johnson-Thompson’s medal hopes were crushed by an awful performance in the javelin, managing a best throw of just 36.36m.
The result ended her challenge for bronze, having seen a dreadful shot put showing rule her out of gold medal contention on day one.
She finished in sixth place with 6,523 points.
Rutherford too could not hide his disappointment at losing his title.
American Jeff Henderson took gold with a final-round effort of 8.38m, denying South Africa’s Luvo Manyonga by a centimetre, and the Briton was down in fourth until producing his best attempt with his last jump.
Even that looked like it would not be enough when another American, Jarrion Lawson, pulled out what looked like a huge effort with the final leap of the competition, but he was ruled to have brushed his hand in the sand as he landed, and the mark was given only as 7.78m.
But it was hard not to feel for the Milton Keynes man, whose fourth-round leap was called a foul only to be reinstated afterwards when replays showed he was perfect on the board. The distance of 8.26m would have put him in the lead at that point.
“I never thought in my career I would be disappointed with bronze, but I’m gutted,” said Rutherford before breaking down for a moment.
“It’s frustrating when you come out of something and you don’t feel you’ve done yourself justice.”