"The certainty was a crucial factor, the certainty that they could deliver," said IOC vice-president Craig Reedie of Britain.
The choice of Tokyo bucked the IOC's recent trend of taking chances on host cities Sochi, Russia, for the 2014 Winter Games, Rio de Janeiro for the 2016 Olympics and Pyeongchang, South Korea, for the 2018 Winter Games.
Preparations for Sochi have been overshadowed by cost overruns, a record US$51 billion ($63 billion) budget, security worries and an international outcry over Russia's anti-gay legislation. There are mounting concerns among the IOC over construction delays in Rio.
The IOC's desire for a reliable, dependable host in 2020 was a crucial factor for Tokyo.
"For better or worse, we picked Sochi followed by Rio followed by Pyeongchang," Canadian member Dick Pound said. "Maybe we need to say, 'all right, whether it's the most exciting city in the world or not, they will deliver'."
Tokyo had been on the defensive in the final days of the campaign because of mounting concerns over the leak of radioactive water from the tsunami-crippled Fukushima nuclear plant.
In the final presentation, Abe gave the IOC assurances that the Fukushima leak was not a threat to Tokyo and took personal responsibility for keeping the games safe.
"Let me assure you the situation is under control," Abe said. "It has never done and will never do any damage to Tokyo."
Abe gave further assurances when pressed on the issue by Norwegian IOC member Gerhard Heiberg.
"It poses no problem whatsoever," Abe said in Japanese, adding that the contamination was limited to a small area and had been "completely blocked".
"There are no health-related problems until now, nor will there be in the future," he said. "I make the statement to you in the most emphatic and unequivocal way."
IOC members said Abe's answers were critical and helped dispel any doubts.
"People wanted to hear it and needed to hear it," Pound said. "And he delivered on that. I think that was a real knockout answer."
Tokyo Electric Power, Fukushima's operator, has acknowledged that tons of radioactive water has been seeping into the Pacific from the plant for more than two years after the March 2011 earthquake and tsunami led to meltdowns at three of its reactors. Recent leaks from tanks storing radioactive water used to cool the reactors have added to fears that the amount of contaminated water is getting out of hand.
Tokyo's bid benefited from Japan's large economy and link to Olympic sponsors. Asia offers a huge market for the IOC.
"There are a lot of commercial advantages for the IOC going to a country with the third-biggest GDP," Australian member John Coates said. "And then compare that to the economic uncertainty facing Spain and the political unrest that Istanbul experienced a few months ago."
Tokyo delegates in the hall screamed with joy after Rogge opened a sealed envelope and read the words: "The International Olympic Committee has the honour of announcing that the games of the 32nd Olympiad in 2020 are awarded to the city of Tokyo."
Even though it was 5am on Sunday in Japan, about 1200 dignitaries and Olympic athletes who crowded into a convention hall in downtown Tokyo celebrated the news.
Cheers of "Banzai!" filled the hall when the announcement was made. In Istanbul's old city, a groan went through a gathering of hundreds of people.
In the first round, Istanbul and Madrid tied with 26 votes each. Tokyo had 42 votes, six short of a winning majority. Istanbul then beat Madrid 49-45 in a tiebreak to advance to the final, which Tokyo won easily.
After Madrid lost the tiebreak, a deathly hush fell over a crowd that had assembled in the Spanish capital's Puerta de Alcala square and the music stopped.
In their final presentations, Madrid made its case as the least expensive option and Istanbul spoke of the historic opportunity to bring the Olympics to a predominantly Muslim country for the first time.
Madrid, bidding for a third straight time, had seemed to have gained the most momentum in recent weeks despite Spain's economic crisis and 27 per cent unemployment rate. The Madrid team claimed the games would pose no financial risk because most of the venues were already built.
- AP