The elite men's and women's races were won by Uganda's Jacob and Hellen Obiri.
A minute's silence was held and the national anthem was played before the start of the elite men's race.
Brendan Foster said the Great North Run was about coming together.
He said that people wanted to come together in moments of mourning.
It was in line with the wishes of the Queen, who wanted people to come together as a community and raise money for charity.
Obiri won the elite women's race in a time of one hour seven minutes and five seconds for her second consecutive Great North Run title.
Jepchirchir was two seconds behind, while Ayana was third. Britain's Charlotte Purdue was in the top five.
The men's elite race was won by two-time Commonwealth Games gold medal winner Eliud Kiplimo, who finished in 59 minutes 33 seconds.
Kenenisa Bekele and Selemon Barega were both runners up in the Olympics.
The men's and women's wheelchair races were won by Commonwealth Games silver medallists.
There was a good atmosphere but it was still sad.
It's nice to get my first win under the King's flag, so it's a proud moment.
The world's biggest half marathon attracted 60,000 entrants.
The Great North Run returned to its usual route after changes were made to make it safer.
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