The 29-year-old Russian was the only athlete still eligible to win the prize. Lebedeva still must participate in the Sept. 9-10 final in Monaco to ensure she collects her money.
The jackpot goes to athletes who sweep their events at all six Golden League meets. The prize was open to 12 events this season.
Lebedeva did it alone this year and became only the second athlete to claim the full jackpot, after 800-meter runner Maria Mutola in 2003.
"It's a great moment, I am overwhelmed," Lebedeva said.
A mother of a three-year-old daughter, Lebedeva said before the meet she would donate 10 percent of the prize to her old school in Volgograd.
Wearing a starting bib with the number 1,000,000, Lebedeva cleared only 13.95 meters in her first leap to begin the competition in fourth place. But her second effort of 14.85 put her into the lead for good.
In the sixth and final series, Yamile Aldama of Sudan soared 14.82 to come close - but not enough to threaten Lebedeva's sweep. Yargelis Savigne of Cuba, silver medalist at last month's world championship in Helsinki, was third at 14.57.
Lebedeva's task was made easier by the late withdrawal of world champion Trecia Smith of Jamaica because of injury.
Nursing a tender Achilles' tendon, Lebedeva pulled out of the Helsinki final in a bid to avoid aggravating the injury. In doing so, she missed the chance of a third straight world title.
Lebedeva, the Olympic long jump champion, and Smith have both jumped 15.11 meters this season, the best in the world. Lebedeva had won the previous Golden League meets in Paris, Rome, Oslo, Zurich and Brussels.
"I feel I am dreaming," Lebedeva said Sunday. "Today is the lucky day for me. The fortune is smiling. I think I made a good decision to save my energy and not jump in the Helsinki final. It was not easy, but I did it. Now I do not need to worry about my family, my daughter, our future."
Christine Arron of France saw her hopes of a share of the jackpot ruined by her defeat in Zurich, the fourth stop of the Golden League tour.
She won Sunday's 100-meter sprint in 11.01 seconds, coming one victory short of being eligible for the jackpot.
"My form seems to be peaking at the end of the season, it's a little bit late," said Arron, who was world bronze medalist.
World champion Lauryn Williams of the United States, who won the Zurich race, finished fourth this time.
Chandra Sturrup of Bahamas was second in 11.02, while Melisa Barber of the United States came third in 11.16. Williams clocked 11.17.
After an often cool and rainy summer in Europe, the final Golden League meet took place in warm and sunny weather in Berlin's Olympic stadium, which will stage next year's soccer World Cup final.
Jamaicans dominated the men's sprints.
Dwight Thomas won the 100 in 10.01 seconds, with Ronald Pognon of France second in 10.08. Jason Gardener of Britain was third in 10.09. Olympic and world champion Justin Gatlin of the United States skipped the meet.
Christopher Williams beat second-placed Tyree Washington of the United States to win the 200 in 20.33. Washington clocked 20.43.
"It was a good race. I came here with the intention to win - so I won," Williams said.
Dominique Arnold of the United States won the 110 hurdles in 13.20, while world champion Ladji Doucoure was sixth. Thomas Blaschek of Germany was second in 13.33 and Robert Kronberg of Sweden took third in 13.55.
Several other world champions also had a bad day.
Rachid Ramzi, the Moroccan now running for Bahrain who swept the 800 and 1,500 titles in Helsinki, finished fourth in the 800. Mbulaeni Mulaudzi of South Africa won in 1:44.26.
In the men's high jump, world champion Yuriy Krymarinko cleared 2.27 meters to finish fourth. Yaroslav Rybakov of Russia, world bronze medalist, won the event at 2.32.
Daniel Kipchirchir Komen of Kenya won his fourth 1,500-meter race in six Golden League meets this year, clocking 3:29.72, the second fastest time this season.
Bernard Lagat of the United States won the 5,000 in a personal best 12:59.29.
Sandra Glover of the United States, the bronze medalist in Helsinki, won the 400 hurdles in 54.17.