Power was restored before noon, Kyodo News agency reported.
Authorities said more than 100,000 people were affected by the train delays, and the outage shut down 900 elevators in the capital region, trapping several dozen with people inside. Officials said most if not all the occupants were rescued soon afterward.
The crane that caused the blackout was perched on a barge travelling on the Kyu Edo River on the eastern edge of Tokyo when it hit power lines spanning the river, shorting them out, said Kiyohito Yokoi, a Tokyo Power Electric Co. official.
The outage, which struck at 0738 (2238GMT), cut electricity to about 1.39 million households in Tokyo and the suburbs of Chiba and Kanagawa, up from the previously announced 800,000 households, according to Naoko Haruyama, another Tokyo Power official.
Public broadcaster NHK reported that the crane was to be used for a construction work and workers aboard the ship did not realise that the 33-meter (109 feet) crane was raised too high.
"We heard a huge explosion. After the crane hit the power lines the second time, we saw blue sparks," a witness told NHK.
The severed power lines are part of a massive grid serving the 35 million inhabitants of the Tokyo metropolitan region, which includes the cities of Yokohama and Chiba. A quarter of Japan's population of 127 million lives there.
The last time Tokyo had a similar blackout was in November 1999, when power was cut to some 800,000 households when a Japanese military plane hit power lines.
"We heard a huge explosion. After the crane hit the power lines the second time, we saw blue sparks"
The number of people affected by the transportation delays on Monday was limited by the four-day "bon" summer holiday, or "day of the dead," and the number of passengers during the morning rush hour was far fewer than usual.
Trading at the Tokyo Stock Exchange began as usual despite the blackout. TSE spokeswoman Mariko Saito said that the bourse, located in central Tokyo, had switched to emergency power sources when the blackout occurred.
The power outages also delayed the openings of the Tokyo Disneyland and DisneySea parks - located in Chiba - by 52 minutes, said Masami Shimomura, spokeswoman for Oriental Land Co., which operates the theme parks.
Nine of Disneyland's 42 attractions and four of DisneySea's 24 had resumed normal operations by mid-morning, Shimomura said. Oriental Land did not yet know how many visitors had been affected by the delay, she said.