The crowd of about 500 people staging a rally at the base of the city landmark - which was lit up in Olympic colors in hopes of celebrating the win - let out a collective cheer when Chicago was surprisingly eliminated in the first round.
But the hopes of a Japanese upset were quickly dashed when the next city to be cut by the International Olympic Committee was Tokyo.
The IOC picked Rio de Janeiro as the 2016 host in the final vote held well past midnight Japanese time, beating out Madrid.
"It's a disappointing outcome. I'm very sorry about it," said Tokyo Vice Governor Hiroshi Sato. "So many people offered their support. I'm at a loss for words. The frustration is that we can't give our stage of dreams to our youth. We tried hard and did everything we could."
Others expressed hopes that Tokyo would bid again.
"It's disappointing, but we're aiming for 2020," said Kenta Takaya, a 33-year-old event planner.
Tokyo spent 15 billion yen ($166 million) promoting itself for the games, which can potentially bring in billions of dollars in tourism revenues, construction projects and sponsorships.
Japanese organizers were eager to bring the Olympics back to Tokyo, whose 1964 games marked Japan's emergence on the international stage after its recovery from defeat in World War II. The country also hosted two winter games - in Sapporo in 1972 and Nagano in 1998.
Newly elected Prime Minister Yukio Hatoyama flew to Copenhagen to give a speech during Tokyo's 45-minute final presentation. Picking up on the bid's long-standing themes of safety and green credentials, he said Tokyo would "show the world how a major metropolis shall flourish without detriment to the environment."
Japanese organizers stressed the financial stability of their bid. With a projected cost of $2.8 billion, bid officials said Tokyo was in a better position than other cities to meet the expenses of hosting a post-recession Olympics. The city said it had already set aside $4 billion to cover the cost of infrastructure development.
Tokyo also boasted what it called the most compact bid among the four cities with almost all venues within 8 kilometers (5 miles) of the main stadium. 23 of its proposed 34 venues already existed and land was secured for the 11 new facilities with a proposed, futuristic 100,000-seat stadium on a pier in Tokyo Bay at the center of the games.
The city wanted to use the games to redevelop a rundown area previously used for industry and shipping, revitalizing the waterfront with housing, retail, and entertainment venues, some from land reclaimed from Tokyo Bay.
But Tokyo's bid has been dogged by lukewarm public support, particularly early in its campaign. An IOC poll in February found only 55 percent of residents supported the effort, the lowest of the four candidate cities.
During an IOC visit to the Japanese capital in April, protesters greeted the inspection team with signs that read: "We don't need the Olympics."
In recent weeks, enthusiasm seemed to grow, with 400,000 people marching through the streets of Tokyo last month to show their support.
"I'm so disappointed," said Yuko Arimori, a silver and bronze medalist in the women's marathon who was at an Olympic event at Tokyo government offices. "It was an important experience for everyone in Tokyo. Let's use this experience to bid again."