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Chopra won the DL trophy in 2022 before finishing second last year.
Amos Serem of Kenya emerged champion in men's 3000m steeplechase.
The finale will be a two-day affair on September 13 and 14 in Brussels.
The Olympic champion gave a best effort of 88.36m, which was just 2 cm short of Jakub Vadlejch's winning throw.
Chopra will now head to the Hangzhou Asian Games where he will defend the gold he had won in 2018 in Indonesia.
Kipyegon, who was embraced by her fellow competitors after the race, has now broken three world records in just two months, including the 1500m and 5000m.
Faith Kipyegon broke the 5,000m world record, a week after becoming the fastest woman ever over 1,500m.
The 24-year-old Keralite is the third Indian after discus thrower Vikas Gowda and javelin thrower Neeraj Chopra to secure a top-three finish in the Diamond League.
The Indian ace finished first in men's javelin throw with a best of 88.67m.
Olympic javelin champion Chopra became the first Indian to win the Diamond League trophy.
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