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Chopra will now head to the Hangzhou Asian Games where he will defend the gold he had won in 2018 in Indonesia.
The Indian star's best effort was 15 centimetres short of Vadlejch's best throw on the night.
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.
The Olympic champion's 88.44m fetched him the gold in the finals in Zurich early on Friday.
Chopra became the first Indian to win a Diamond League meet with an 89.08m throw in Lausanne on Friday night.
The Olympic gold medallist's first attempt of 89.08m on his first attempt.