Fighting on the undercard of undisputed super-bantamweight world champion Naoya "Monster" Inoue's title fight against Mexico's Luis Nery, Takei started strongly before Moloney came back into the bout in his second title defence.
But the Japanese fighter, a former kickboxer who had won all eight of his previous boxing matches by knockout, took the title in front of a raucous crowd at the 45,000-plus seater venue.
"The 12th round was a real struggle," said the 27-year-old Takei.
"I wanted to win by knock-out but Moloney was really tough.
"I knew he was strong before the fight and I trained really hard because of that -- it's thanks to Moloney that I was able to toughen up," he added.
Moloney, who won the vacant title in May last year, saw his record drop to 29-3, with 27 wins by KO.
Earlier on the undercard, Inoue's younger brother Takuma Inoue defended his WBA bantamweight title with a unanimous decision win over fellow Japanese Sho Ishida.
Ishida floored Inoue in the first round with a left jab but the champion recovered to dominate the fight.
Japan's Seigo Yuri Akui defended his WBA flyweight title with a unanimous decision win over countryman Taku Kuwahara.
Boxing was returning to the Tokyo Dome for the first time since 42-1 underdog James "Buster" Douglas knocked out unbeaten heavyweight champion Mike Tyson in February 1990 in one of the sport's biggest upsets.
The unbeaten Naoya Inoue (26-0, 23 KOs) puts his four super-bantamweight titles on the line in the main event against Nery, a former two-division world champion.
