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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.
Find out about how to get into running with our special guide.

Police had appealed for witnesses to an incident in the town's Agnew Crescent on Saturday evening.
However, a short statement said a 23-year-old man had now been arrested and charged with wasting police time.
It added that they were not looking for anyone in respect of the original alleged robbery.

St James' Park and West Ham United's ground were raided in April by HM Revenue and Customs as part of a Â£5m National Insurance fraud investigation.
Newcastle's managing director Lee Charnley was among several men arrested and later released without charge.
The ban remains in force until a court hearing on 22 June.
High Court judge Mr Justice Supperstone imposed the ban after lawyers for Newcastle United applied for a judicial review against HMRC.
He directed that any material retained by HMRC must be returned to the club.
He also directed that the legal action involving the Magpies, who have just secured promotion to the Premier League, must return to court on 22 June.
It is expected the club will then have to show that it has an arguable case to take to a full judicial review hearing.
No details of the grounds of the challenge were revealed during Thursday's short court hearing.
Lawyers for both the club and HMRC said they could not provide any further information.
During the raids HMRC said it had seized business records and financial records as well as computers and mobile phones.
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.
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A man has been charged with wasting police time following inquiries into an alleged assault with intent to rob in Stranraer.
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Tax officials have been banned from examining material seized from Newcastle United's ground, following a legal challenge mounted by the club.