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Rutherford, 29, triumphed with a leap of 7.66m, with Uruguay's Emiliano Lasa second and GB's Daniel Gardiner third.
Briton Laura Muir won the one-mile event nine days after sealing the Diamond League title in Zurich.
The 23-year-old, who was seventh in the Olympic 1500m final, told BBC One: "I'm over the moon with the season."
She added: "Apart from the glitch in the Olympics, it's been good. To finish my season on home soil is great."
Kenya's Olympic 800m champion David Rudisha held off Ireland's Mark English for victory in the 500m, while James Dasaolu won the 100m in a photo finish with fellow Briton Chijindu Ujah.
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Dasaolu, who, like Ujah, reached the semi-finals n Rio, said: "It was neck and neck all the way. It was just my lucky day today."
Desiree Henry set a new British record of 16.57 seconds in winning the women's 150m, as Jake Wightman won the men's one-mile race in four minutes 5.70 seconds.
He said: "It's been a hard last month since the European Championships in July. I wanted to keep going. This is the fun part of the season."
Mo Farah, who is aiming to become the first man to win three consecutive Great North Run titles on Sunday, was presented to the crowd on Saturday.
The two-time Olympic 5,000m and 10,000m champion said: "I just want to take it all in. I can't believe how much support I've had. Everywhere I go, it's 'Mo, Mo, Mo'."
Click here for full results from Saturday's Great North City Games in Newcastle.
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Britain's Greg Rutherford won the long jump at the Great North City Games in Newcastle, in his first competition since winning Olympic bronze in Rio.