The Japanese 24-year-old took scorecards of 117-109, 116-110 and 114-112 over his Mexican opponent in Takamatsu, despite being docked two points for two low blows in the fifth and 11th rounds.
He joins 26-year-old WBA bantamweight champion Koki Kameda, a three-division world champion, and 22-year-old WBO bantamweight titlist Tomoki Kameda in a history-making litter.
Daiki, 24, won his second world title and improved to 29-3 with 18 KOs. He previously held the WBA flyweight title.
The brothers are a combined 88-4 with 53 KOs and all hold world championships.
Heavyweight brothers Wladimir and Vitali Klitschko are also current champions together, with the Ukrainian powerhouses dominating the heavyweight ranks.
The Marquez brothers, Juan Manuel and Rafael, also held belts simultaneously. No family previously, though, had three siblings as champions at the same time until the Kameda brothers.
The vacant WBA interim junior bantamweight crown was decided on the same day in Bangkok, Thailand, where Denkaosan Kaovichit claimed a split decision over fellow former WBA super-fly champion Nobuo Nashiro.
And at the weekend, Adrian Hernandez retained his WBC light-flyweight strap over Atsushi Kakutani in Mexico City with a fourth-round TKO.
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